Markers of definitive endoderm

ABSTRACT

Disclosed herein are reagent-cell complexes comprising one or more definitive endoderm cells. Also described herein are compositions for detecting definitive endoderm. Method of enriching, isolating and/or purifying definitive endoderm cells are also disclosed.

RELATED APPLICATIONS

This application is a U.S. national phase application under 35 U.S.C. §371 of International Application No. PCT/US2006/043932, entitled MARKERS OF DEFINITIVE ENDODERM, filed Nov. 13, 2006, designating the United States and published in English on May 24, 2007 as WO2007/059007, which is a nonprovisional application claiming priority under 35 U.S.C. §119(e) to U.S. Provisional Patent Application No. 60/736,598, entitled MARKERS OF DEFINITIVE ENDODERM, filed Nov. 14, 2005; this application is also a continuation-in-part of U.S. patent application Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004, which claims priority under 35 U.S.C. §119(e) as a nonprovisional application to U.S. Provisional Patent Application No. 60/587,942, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 14, 2004; and U.S. Provisional Patent Application No. 60/586,566, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 9, 2004, and U.S. Provisional Patent Application No. 60/532,004, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2003. The disclosure of each of the foregoing priority applications is incorporated herein by reference in its entirety

FIELD OF THE INVENTION

The present invention relates to the fields of medicine and cell biology. In particular, the present invention relates to the identification and isolation of definitive endoderm cells.

BACKGROUND

Human pluripotent stem cells, such as embryonic stem (ES) cells and embryonic germ (EG) cells, were first isolated in culture without fibroblast feeders in 1994 (Bongso et al., 1994) and with fibroblast feeders (Hogan, 1997). Later, Thomson, Reubinoff and Shamblott established continuous cultures of human ES and EG cells using mitotically inactivated mouse feeder layers (Reubinoff et al., 2000; Shamblott et al., 1998; Thomson et al., 1998).

Human ES and EG cells (hESCs) offer unique opportunities for investigating early stages of human development as well as for therapeutic intervention in several disease states, such as diabetes mellitus and Parkinson's disease. For example, the use of insulin-producing P-cells derived from hESCs would offer a vast improvement over current cell therapy procedures that utilize cells from donor pancreases for the treatment of diabetes. However, presently it is not known how to generate an insulin-producing β-cell from hESCs. As such, current cell therapy treatments for diabetes mellitus, which utilize islet cells from donor pancreases, are limited by the scarcity of high quality islet cells needed for transplant. Cell therapy for a single Type I diabetic patient requires a transplant of approximately 8×10⁸ pancreatic islet cells. (Shapiro et al., 2000; Shapiro et al., 2001a; Shapiro et al., 2001b). As such, at least two healthy donor organs are required to obtain sufficient islet cells for a successful transplant. Human embryonic stem cells offer a source of starting material from which to develop substantial quantities of high quality differentiated cells for human cell therapies.

Two properties that make hESCs uniquely suited to cell therapy applications are pluripotence and the ability to maintain these cells in culture for prolonged periods. Pluripotency is defined by the ability of hESCs to differentiate to derivatives of all 3 primary germ layers (endoderm, mesoderm, ectoderm) which, in turn, form all somatic cell types of the mature organism in addition to extraembryonic tissues (e.g. placenta) and germ cells. Although pluripotency imparts extraordinary utility upon hESCs, this property also poses unique challenges for the study and manipulation of these cells and their derivatives. Owing to the large variety of cell types that may arise in differentiating hESC cultures, the vast majority of cell types are produced at very low efficiencies. Additionally, success in evaluating production of any given cell type depends critically on defining appropriate markers. Achieving efficient, directed differentiation is of great importance for therapeutic application of hESCs.

In order to use hESCs as a starting material to generate cells that are useful in cell therapy applications, it would be advantageous to overcome the foregoing problems. For example, it would be useful to identify and isolate cell types, such as definitive endoderm, that can later differentiate into pancreatic islet/P-cells, as well as other useful cell types.

SUMMARY OF THE INVENTION

Embodiments of the present invention relate to methods for producing a cell population enriched in definitive endoderm cells. The method can include the following steps: providing a cell population including definitive endoderm cells with a reagent that binds to a marker selected from Table 3, and separating definitive endoderm cells bound to the reagent from cells that are not bound to the reagent, thereby producing a cell population enriched in definitive endoderm cells. In some embodiments, the marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In preferred embodiments, the marker is selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. The reagent used to produce a cell population enriched in definitive endoderm can be an antibody, such as a polyclonal or monoclonal antibody that binds to one of the markers described herein.

In certain embodiments, the method of producing a cell population enriched for definitive endoderm cells can also include the following steps: obtaining a cell population comprising pluripotent human cells; providing the cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to definitive endoderm cells; and allowing sufficient time for definitive endoderm cells to form. In further embodiments, the at least one growth factor can be selected from the following: Nodal, activin A, activin B and combinations thereof. In some embodiments, the at least one growth factor can be provided to said cell population at a concentration ranging from about 1 ng/ml to about 1000 ng/ml. In further preferred embodiments, the at least one growth factor can be provided in a concentration of at least about 100 ng/ml. In other preferred embodiments, the cell population can be grown in a medium including less than about 10% serum. In yet other preferred embodiments, the pluripotent human cells can be human embryonic stem cells.

Additional embodiments of the invention relate to other methods of producing a cell population enriched in definitive endoderm cells, which can include the steps of: obtaining a population of pluripotent cells, wherein at least one cell of the pluripotent cell population includes a nucleic acid encoding a fluorescent protein or a biologically active fragment thereof, which has been operably linked to a promoter that controls the expression of a marker selected from Table 3; differentiating the pluripotent cells so as to produce definitive endoderm cells, wherein the definitive endoderm cells express said fluorescent protein; and separating the definitive endoderm cells from cells that do not substantially express said fluorescent protein. In preferred embodiments, the marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other embodiments, the marker is selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. Methods known in the art, such as fluorescence activated cell sorting (FACS), can be used to separate the fluorescently-tagged definitive endoderm cells from cells that do not substantially express said fluorescent protein.

In some embodiments, the step of differentiating the pluripotent cells can include providing the cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to definitive endoderm cells, and allowing sufficient time for definitive endoderm cells to form. For example, in some embodiments, the cell population can be provided with at least one growth factor selected from the group consisting of Nodal, activin A, activin B and combinations thereof. In preferred embodiments, the at least one growth factor can be provided to said cell population at a concentration ranging from about 1 ng/ml to about 1000 ng/ml. In other preferred embodiments, the at least one growth factor can be provided in a concentration of at least about 100 ng/ml. In still other preferred embodiments, the cell population can be grown in a medium including less than about 10% serum. In yet other preferred embodiments, the pluripotent human cells can be human embryonic stem cells.

In some embodiments, methods, such as affinity-based separation or magnetic-based separation, are used to enrich, isolate or substantially purify preparations of definitive endoderm cells which bind to the reagent.

In accordance with the methods described herein, embodiments of the present invention relate to compositions useful for the enrichment and isolation of definitive endoderm cells. Some embodiments relate to an ex vivo reagent-cell complex. The ex vivo complex can include a human definitive endoderm cell expressing a marker selected from Table 3 and a reagent bound to the marker. The definitive endoderm cell of the ex vivo reagent-cell complex is a multipotent cell that can differentiate into cells of the gut tube or organs derived therefrom. In certain embodiments, the marker expressed by the human definitive endoderm cell is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In preferred embodiments, the definitive endoderm cell expresses a cell-surface marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

The reagent of the reagent-cell complex can be, for example, an antibody. In preferred embodiments, the bound marker in the reagent-cell complex can be a cell-surface marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

In accordance with the embodiments described herein, aspects of the present invention relate to compositions of cell populations that include human cells wherein at least about 10% of the cells are reagent-cell complexes, wherein the complex can include a human definitive endoderm cell expressing a marker selected from Table 3, and wherein the definitive endoderm cell is a multipotent cell that can differentiate into cells of the gut tube or organs derived therefrom. In such embodiments, the marker is expressed by the definitive endoderm cell, wherein the marker is selected from Table 3, and a reagent bound to the marker. In some embodiments, the marker bound by the reagent in the reagent-cell complex is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In preferred embodiments, the marker bound by the reagent is selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. In further embodiments, the expression of one or more of the markers selected from Table 3 in definitive endoderm cells can be greater than expression of a marker selected from the group consisting of OCT4, AFP, Thrombomodulin (TM), SPARC and SOX7.

In some embodiments, the cell population includes human cells wherein at least about 20% of the cells are reagent-cell complexes as described herein. In other embodiments, the cell population includes human cells wherein at least about 40% of the cells are reagent-cell complexes as described herein. In yet other embodiments, the cell population includes human cells wherein at least about 60% of the cells are reagent-cell complexes as described herein. In yet other embodiments, the cell population includes human cells wherein at least about 80% of the cells are reagent-cell complexes as described herein. In yet other embodiments, the cell population includes human cells wherein at least about 95% of the cells are reagent-cell complexes as described herein.

Additionally, embodiments of the present invention also relate to isolated antibodies that bind to markers that are differentially expressed in definitive endoderm cells. For example, some embodiments relate to any of the markers shown in Table 3. In preferred embodiments, the antibody binds to a polypeptide encoded by AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other preferred embodiments, the antibody binds to a marker that is expressed on the cell surface, such as for example, CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

Antibodies described herein can be either polyclonal or monoclonal. Further, in certain embodiments, the antibodies can be single chain, and/or modified, for example to incorporate a label.

Other embodiments of the present invention relate to compositions for the identification of definitive endoderm. The composition can include a first oligonucleotide that hybridizes to a first marker, wherein the first marker is selected from Table 3; and a second oligonucleotide that hybridizes to a second marker, wherein the second marker is selected from Table 3, and wherein the second marker is different from the first marker. In preferred embodiments, the first marker and the second marker can be selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706, AW772192, OCT4, AFP, Thrombomodulin (TM), SPARC and SOX7. In other preferred embodiments, the first marker and the second marker can be selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In still other preferred embodiments, the first marker and second marker are selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. The compositions above can also include a polymerase, such as an RNA-dependent DNA polymerase and/or a DNA-dependent DNA polymerase. In certain embodiments, at least one oligonucleotide includes a label. In some embodiments, the marker can be a nucleic acid, for example DNA or RNA.

Other embodiments relate to methods of detecting definitive endoderm cells that can include the steps of detecting the presence of definitive endoderm cells in a cell population by detecting expression of at least one marker selected from Table 3 in cells of the cell population. In preferred embodiments, the at least one marker can be selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other preferred embodiments, the method can also include detection of expression of at least one marker selected from the group consisting of OCT4, AFP, TM, SPARC and SOX7 in cells of the cell population. In some embodiments, the expression of the at least one marker selected from Table 3 can be greater than expression of the at least one marker selected from the group consisting of OCT4, AFP, TM, SPARC and SOX7 in the definitive endoderm cells. In further embodiments, the method can also include detecting expression of at least one marker selected from the group consisting of SOX17 and CXCR4, wherein expression of the at least one marker selected from Table 3 and expression of the at least one marker selected from the group consisting of SOX17 and CXCR4 is greater than expression of the at least one marker selected from the group consisting of OCT4, AFP, TM, SPARC and SOX7 in the definitive endoderm cells. In some embodiments, the expression of the at least one marker is determined by quantitative polymerase chain reaction (Q-PCR). In other embodiments, the expression of the at least one marker is determined by immunocytochemistry.

Other embodiments relate to methods of identifying a differentiation factor capable of promoting the differentiation of human definitive endoderm cells in a cell population including human cells. Methods can include the steps of: obtaining a cell population including human definitive endoderm cells, providing a candidate differentiation factor to the cell population, determining expression of a marker selected from Table 3 in the cell population at a first time point, determining expression of the same marker in the cell population at a second time point, wherein the second time point is subsequent to the first time point and wherein the second time point is subsequent to providing said cell population with said candidate differentiation factor and determining if expression of the marker in the cell population at the second time point is increased or decreased as compared to expression of the marker in the cell population at the first time point, wherein an increase or decrease in expression of said marker in the cell population indicate can that said candidate differentiation factor is capable of promoting the differentiation of said human definitive endoderm cells. In preferred embodiments, the marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other embodiments, the human definitive endoderm cells include at least about 10% of the human cells in the cell population. In preferred embodiments, the human definitive endoderm cells include about 90% of the human cells in said cell population. In yet other embodiments, the human definitive endoderm cells can differentiate into cells, tissues or organs derived from the gut tube in response to the candidate differentiation factor.

In embodiments described herein, the first time point can be prior to providing the candidate differentiation factor to the cell population, whereas in other embodiments, the first time point can be at approximately the same time as providing the candidate differentiation factor to the cell population. In still other embodiments, the first time point can be subsequent to providing the candidate differentiation factor to the cell population. In some embodiments, expression of the marker can be determined by quantitative polymerase chain reaction (Q-PCR), whereas in other embodiments, expression of the marker can be determined by immunocytochemistry.

Candidate differentiation factors can include known and unknown factors, and may be small molecules, polypeptides, or the like. In certain embodiments, the candidate differentiation factor can include a growth factor. In some embodiments, the candidate differentiation factor can be provided to the cell population at a concentration of between about 1 ng/ml to about 1 mg/ml. In preferred embodiments, the candidate differentiation factor can be provided to the cell population at a concentration of about 100 ng/ml

Some embodiments of the present invention relate to cell cultures comprising definitive endoderm cells, wherein the definitive endoderm cells are multipotent cells that can differentiate into cells of the gut tube or organs derived from the gut tube. In accordance with certain embodiments, the definitive endoderm cells are mammalian cells, and in a preferred embodiment, the definitive endoderm cells are human cells. In some embodiments of the present invention, definitive endoderm cells express or fail to significantly express certain markers. In some embodiments, one or more markers selected from Table 3 are expressed in definitive endoderm cells. In other embodiments, one or more markers selected from the group consisting of OCT4, alpha-fetoprotein (AFP), Thrombomodulin (TM), SPARC and SOX7 are not significantly expressed in definitive endoderm cells.

In accordance with other embodiments of the present invention, methods of producing definitive endoderm from pluripotent cells are described. In some embodiments, pluripotent cells are derived from a morula. In some embodiments, pluripotent cells are stem cells. Stem cells used in these methods can include, but are not limited to, embryonic stem cells. Embryonic stem cells can be derived from the embryonic inner cell mass or from the embryonic gonadal ridges. Embryonic stem cells can originate from a variety of animal species including, but not limited to, various mammalian species including humans. In a preferred embodiment, human embryonic stem cells are used to produce definitive endoderm. In certain embodiments the hESCs are maintained on a feeder layer. In such embodiments, the feeder layer cells can be cells, such as fibroblasts, which are obtained from humans, mice or any other suitable organism.

In some embodiments of the present invention, the compositions comprising definitive endoderm cells and hESCs also includes one or more growth factors. Such growth factors can include growth factors from the TGFβ superfamily. In such embodiments, the one or more growth factors comprise the Nodal/Activin and/or the BMP subgroups of the TGFβ superfamily of growth factors. In some embodiments, the one or more growth factors are selected from the group consisting of Nodal, Activin A, Activin B, BMP4, Wnt3a or combinations of any of these growth factors

In certain jurisdictions, there may not be any generally accepted definition of the term “comprising.” As used herein, the term “comprising” is intended to represent “open” language which permits the inclusion of any additional elements. With this in mind, additional embodiments of the present inventions are described with reference to the numbered paragraphs below:

1. An isolated antibody that binds to a marker selected from Table 3.

2. The antibody of paragraph 1, wherein said marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

3. The antibody of paragraph 2, wherein said marker comprises a polypeptide selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

4. The antibody of paragraph 1, wherein said antibody is polyclonal.

5. The antibody of paragraph 1, wherein said antibody is monoclonal.

6. The antibody of paragraph 1, wherein said antibody is a single-chain antibody.

7. The antibody of paragraph 1, wherein said antibody is labeled.

8. An ex vivo reagent-cell complex comprising a human definitive endoderm cell expressing a marker selected from Table 3, said definitive endoderm cell being a multipotent cell that can differentiate into cells of the gut tube or organs derived therefrom, and a reagent bound to said marker.

9. The reagent-cell complex of paragraph 8, wherein said marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

10. The reagent-cell complex of paragraph 9, wherein said marker comprises a polypeptide selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

11. The reagent-cell complex of paragraph 10, wherein said reagent comprises an antibody.

12. The reagent-cell complex of paragraph 10, wherein said reagent comprises a ligand for a receptor.

13. A cell population comprising human cells wherein at least about 10% of said cells form reagent-cell complexes according to paragraph 8.

14. A cell population comprising human cells wherein at least about 20% of said cells form reagent-cell complexes according to paragraph 8.

15. A cell population comprising human cells wherein at least about 40% of said cells form reagent-cell complexes according to paragraph 8.

16. A cell population comprising human cells wherein at least about 60% of said cells form reagent-cell complexes according to paragraph 8.

17. A cell population comprising human cells wherein at least about 80% of said cells form reagent-cell complexes according to paragraph 8.

18. A cell population comprising human cells wherein at least about 95% of said cells form reagent-cell complexes according to paragraph 8.

19. The cell population of any one of paragraphs 13-18, wherein said marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

20. The cell population of paragraph 19, wherein expression of said marker is greater than expression of a marker selected from the group consisting of OCT4, AFP, Thrombomodulin (TM), SPARC and SOX7 in definitive endoderm cells.

21. The cell population of paragraph 19, wherein said marker comprises a polypeptide selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

22. The cell population of paragraph 20, wherein said reagent comprises an antibody.

23. The cell population of paragraph 20, wherein said reagent comprises a ligand for a receptor.

24. A composition for the identification of definitive endoderm, said composition comprising a first oligonucleotide that hybridizes to a first marker, wherein said first marker is selected from the group consisting of Table 3, OCT4, AFP, Thrombomodulin (TM), SPARC and SOX7, and a second oligonucleotide that hybridizes to a second marker, wherein said second marker is selected from the group consisting of Table 3, OCT4, AFP, Thrombomodulin (TM), SPARC and SOX7, and wherein said second marker is different from said first marker.

25. The composition of paragraph 24, wherein said first marker and said second marker are selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706, AW772192, OCT4, AFP, Thrombomodulin (TM), SPARC and SOX7.

26. The composition of paragraph 25, wherein said first marker and said second marker are selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

27. The composition of paragraph 24, wherein said marker is a nucleic acid.

28. The composition of paragraph 27, wherein said nucleic acid is DNA.

29. The composition of paragraph 27, wherein said nucleic acid is RNA.

30. The composition of paragraph 24, wherein at least one oligonucleotide comprises a label.

31. The composition of paragraph 24 further comprising a polymerase.

32. The composition of paragraph 31, wherein the polymerase comprises a DNA-dependent DNA polymerase.

33. The composition of paragraph 31, wherein the polymerase comprises an RNA-dependent DNA polymerase.

34. The method of paragraph 33, wherein the RNA-dependent DNA polymerase comprises Moloney Murine Leukemia Virus reverse transcriptase or Avian Myeloblastosis Virus (AMV) reverse transcriptase.

35. A method for producing a cell population enriched in definitive endoderm cells, said method comprising the steps of providing a cell population comprising definitive endoderm cells with a reagent that binds to a marker selected from Table 3, and separating definitive endoderm cells bound to said reagent from cells that are not bound to said reagent, thereby producing a cell population enriched in definitive endoderm cells.

36. The method of paragraph 35, wherein said marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

37. The method of paragraph 36, wherein the marker is selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

38. The method of paragraph 37, wherein said reagent comprises an antibody or a ligand for a receptor.

39. The method of paragraph 35 further comprising the steps of obtaining a cell population comprising pluripotent human cells, providing said cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to definitive endoderm cells, and allowing sufficient time for definitive endoderm cells to form.

40. The method of paragraph 39, wherein said at least one growth factor is selected from the group consisting of Nodal, activin A, activin B and combinations thereof.

41. The method of paragraph 40, wherein said at least one growth factor is provided to said cell population at a concentration ranging from about 1 ng/ml to about 1000 ng/ml.

42. The method of paragraph 41, wherein said at least one growth factor is provided in a concentration of at least about 100 ng/ml

43. The method of paragraph 39, wherein said cell population is grown in a medium comprising less than about 10% serum.

44. The method of paragraph 39, wherein said pluripotent human cells are human embryonic stem cells.

45. A method of producing a cell population enriched in definitive endoderm cells, said method comprising the steps of obtaining a population of pluripotent cells, wherein at least one cell of said pluripotent cell population comprises a nucleic acid encoding a fluorescent protein or a biologically active fragment thereof, which has been operably linked to a promoter that controls the expression of a marker selected from Table 3, differentiating said pluripotent cells so as to produce definitive endoderm cells, wherein said definitive endoderm cells express said fluorescent protein, and separating said definitive endoderm cells from cells that do not substantially express said fluorescent protein.

46. The method of paragraph 45, wherein said marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

47. The method of paragraph 45, wherein fluorescence activated cell sorting (FACS) is used to separate said definitive endoderm cells from said cells that do not substantially express said fluorescent protein.

48. The method of paragraph 45, wherein said step of differentiating said pluripotent cells further comprises providing said cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to definitive endoderm cells, and allowing sufficient time for definitive endoderm cells to form.

49. The method of paragraph 48, wherein said at least one growth factor is selected from the group consisting of Nodal, activin A, activin B and combinations thereof.

50. The method of paragraph 49, wherein said at least one growth factor is provided to said cell population at a concentration ranging from about 1 ng/ml to about 1000 ng/ml.

51. The method of paragraph 50, wherein said at least one growth factor is provided in a concentration of at least about 100 ng/ml

52. The method of paragraph 45, wherein said cell population is grown in a medium comprising less than about 10% serum.

53. The method of paragraph 45, wherein said pluripotent human cells are human embryonic stem cells.

54. A method of detecting definitive endoderm cells, said method comprising detecting the presence of definitive endoderm cells in a cell population by detecting expression of at least one marker selected from Table 3 in cells of said cell population.

55. The method of paragraph 54, wherein said at least one marker is selected from a group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

56. The method of paragraph 54 further comprising detecting expression of at least one marker selected from the group consisting of OCT4, AFP, TM, SPARC and SOX7 in cells of said cell population, wherein the expression of said at least one marker selected from Table 3 is greater than the expression of said at least one marker selected from the group consisting of: OCT4, AFT, TM, SPARC and SOX7 in said definitive endoderm cells.

57. The method of Paragraph 54, further comprising detecting expression of at least one marker selected from the group consisting of SOX17 and CXCR4, and at least one marker from Table 3 other than SOX17 and CXCR4, wherein expression of said at least one marker selected from Table 3 other than SOX17 and CXCR4 and expression of said at least one marker selected from the group consisting of SOX17 and CXCR4 is greater than the expression of said at least one marker selected from the group consisting of OCT4, AFP, TM, SPARC and SOX7 in said definitive endoderm cells.

58. The method of paragraph 54, wherein expression of said at least one marker is determined by quantitative polymerase chain reaction (Q-PCR).

59. The method of paragraph 54, wherein expression of said at least one marker is determined by immunocytochemistry.

60. A method of identifying a differentiation factor capable of promoting the differentiation of human definitive endoderm cells in a cell population comprising human cells, said method comprising the steps of obtaining a cell population comprising human definitive endoderm cells, providing a candidate differentiation factor to said cell population, determining expression of a marker selected from Table 3 in said cell population at a first time point, determining expression of the same marker in said cell population at a second time point, wherein said second time point is subsequent to said first time point and wherein said second time point is subsequent to providing said cell population with said candidate differentiation factor, and determining if expression of the marker in said cell population at said second time point is increased or decreased as compared to expression of the marker in said cell population at said first time point, wherein an increase or decrease in expression of said marker in said cell population indicates that said candidate differentiation factor is capable of promoting the differentiation of said human definitive endoderm cells.

61. The method of paragraph 60, wherein said marker is selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192.

62. The method of paragraph 60, wherein said human definitive endoderm cells comprise at least about 10% of the human cells in said cell population.

63. The method of paragraph 60, wherein said human definitive endoderm cells comprise at least about 90% of the human cells in said cell population.

64. The method of paragraph 60, wherein said human definitive endoderm cells differentiate into cells, tissues or organs derived from the gut tube in response to said candidate differentiation factor.

65. The method of paragraph 60, wherein said first time point is prior to providing said candidate differentiation factor to said cell population.

66. The method of paragraph 60, wherein said first time point is at approximately the same time as providing said candidate differentiation factor to said cell population.

67. The method of paragraph 60, wherein said first time point is subsequent to providing said candidate differentiation factor to said cell population.

68. The method of paragraph 60, wherein expression of said marker is determined by quantitative polymerase chain reaction (Q-PCR).

69. The method of paragraph 60, wherein expression of said marker is determined by immunocytochemistry.

70. The method of paragraph 60, wherein said candidate differentiation factor comprises a small molecule.

71. The method of paragraph 60, wherein said candidate differentiation factor comprises a polypeptide.

72. The method of paragraph 60, wherein said candidate differentiation factor comprises a growth factor.

73. The method of paragraph 60, wherein said candidate differentiation factor is provided to said cell population at a concentration of between about 1 ng/ml to about 1 mg/ml.

74. The method of paragraph 73, wherein said candidate differentiation factor is provided to said cell population at a concentration of about 100 ng/ml.

It will be appreciated that the methods and compositions described above relate to cells cultured in vitro. However, the above-described in vitro differentiated cell compositions may be used for in vivo applications.

Additional embodiments of the present invention may also be found in U.S. Provisional Patent Application No. 60/532,004, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2003; U.S. Provisional Patent Application No. 60/566,293, entitled PDX1 EXPRESSING ENDODERM, filed Apr. 27, 2004; U.S. Provisional Patent Application No. 60/586,566, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 9, 2004; U.S. Provisional Patent Application No. 60/587,942, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 14, 2004; U.S. patent application Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004, and U.S. patent application Ser. No. 11/115,868, entitled PDX1 EXPRESSING ENDODERM, filed Apr. 26, 2005, U.S. patent application Ser. No. 11/165,305, entitled METHODS FOR IDENTIFYING FACTORS FOR DIFFERENTIATING DEFINITIVE ENDODERM, filed Jun. 23, 2005, the disclosures of which are incorporated herein by reference in their entireties.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of a proposed differentiation pathway for the production of beta-cells from hESCs. The first step in the pathway commits the ES cell to the definitive endoderm lineage and represents an early step in the further differentiation of ES cells to pancreatic endoderm, endocrine endoderm, or islet/beta-cell. Some factors useful for mediating this transition are members of the TGFβ family which include, but are not limited to, activins, nodals and BMPs. Exemplary markers for defining the definitive endoderm target cell are SOX17, GATA4, HNF3b, MIXL1 and CXCR4.

FIG. 2 is a diagram of the human SOX17 cDNA which displays the positions of conserved motifs and highlights the region used for the immunization procedure by GENOVAC.

FIG. 3 is a relational dendrogram illustrating that SOX17 is most closely related to SOX7 and somewhat less to SOX18. The SOX17 proteins are more closely related among species homologs than to other members of the SOX group F subfamily within the same species.

FIG. 4 is a Western blot probed with the rat anti-SOX17 antibody. This blot demonstrates the specificity of this antibody for human SOX17 protein over-expressed in fibroblasts (lane 1) and a lack of immunoreactivity with EGFP (lane 2) or the most closely related SOX family member, SOX7 (lane 3).

FIGS. 5A-B are micrographs showing a cluster of SOX17⁺ cells that display a significant number of AFP⁺ co-labeled cells (A). This is in striking contrast to other SOX17⁺ clusters (B) where little or no AFP⁺ cells are observed.

FIGS. 6A-C are micrographs showing parietal endoderm and SOX17. Panel A shows immunocytochemistry for human Thrombomodulin (TM) protein located on the cell surface of parietal endoderm cells in randomly differentiated cultures of hES cells. Panel B is the identical field shown in A double-labeled for TM and SOX17. Panel C is the phase contrast image of the same field with DAPI labeled nuclei. Note the complete correlation of DAPI labeled nuclei and SOX17 labeling.

FIGS. 7A-B are bar charts showing SOX17 gene expression by quantitative PCR (Q-PCR) and anti-SOX17 positive cells by SOX17-specific antibody. Panel A shows that activin A increases SOX17 gene expression while retinoic acid (RA) strongly suppresses SOX17 expression relative to the undifferentiated control media (SR20). Panel B shows the identical pattern as well as a similar magnitude of these changes is reflected in SOX17⁺ cell number, indicating that Q-PCR measurement of SOX17 gene expression is very reflective of changes at the single cell level.

FIG. 8A is a bar chart which shows that a culture of differentiating hESCs in the presence of activin A maintains a low level of AFP gene expression while cells allowed to randomly differentiate in 10% fetal bovine serum (FBS) exhibit a strong upregulation of AFP. The difference in expression levels is approximately 7-fold.

FIGS. 8B-C are images of two micrographs showing that the suppression of AFP expression by activin A is also evident at the single cell level as indicated by the very rare and small clusters of AFP⁺ cells observed in activin A treatment conditions (bottom) relative to 10% FBS alone (top).

FIGS. 9A-B are comparative images showing the quantitation of the AFP⁺ cell number using flow cytometry. This figure demonstrates that the magnitude of change in AFP gene expression (FIG. 8A) in the presence (right panel) and absence (left panel) of activin A exactly corresponds to the number of AFP⁺ cells, further supporting the utility of Q-PCR analyses to indicate changes occurring at the individual cell level.

FIGS. 10A-F are micrographs which show that exposure of hESCs to nodal, activin A and activin B (NAA) yields a striking increase in the number of SOX17⁺ cells over the period of 5 days (A-C). By comparing to the relative abundance of SOX17⁺ cells to the total number of cells present in each field, as indicated by DAPI stained nuclei (D-F), it can be seen that approximately 30-50% of all cells are immunoreactive for SOX17 after five days treatment with NAA.

FIG. 11 is a bar chart which demonstrates that activin A (0, 10, 30 or 100 ng/ml) dose-dependently increases SOX17 gene expression in differentiating hESCs. Increased expression is already robust after 3 days of treatment on adherent cultures and continues through subsequent 1, 3 and 5 days of suspension culture as well.

FIGS. 12A-C are bar charts which demonstrate the effect of activin A on the expression of MIXL1 (panel A), GATA4 (panel B) and HNF3b (panel C). Activin A dose-dependent increases are also observed for three other markers of definitive endoderm; MIXL1, GATA4 and HNF3b. The magnitudes of increased expression in response to activin dose are strikingly similar to those observed for SOX17, strongly indicating that activin A is specifying a population of cells that co-express all four genes (SOX17⁺, MIXL1⁺, GATA4⁺ and HNF3b⁺).

FIGS. 13A-C are bar charts which demonstrate the effect of activin A on the expression of AFP (panel A), SOX7 (panel B) and SPARC (panel C). There is an activin A dose-dependent decrease in expression of the visceral endoderm marker AFP. Markers of primitive endoderm (SOX7) and parietal endoderm (SPARC) remain either unchanged or exhibit suppression at some time points indicating that activin A does not act to specify these extra-embryonic endoderm cell types. This further supports the fact that the increased expression of SOX17, MIXL1, GATA4, and HNF3b are due to an increase in the number of definitive endoderm cells in response to activin A.

FIGS. 14A-B are bar charts showing the effect of activin A on ZIC1 (panel A) and Brachyury expression (panel B) Consistent expression of the neural marker ZIC1 demonstrates that there is not a dose-dependent effect of activin A on neural differentiation. There is a notable suppression of mesoderm differentiation mediated by 100 ng/ml of activin A treatment as indicated by the decreased expression of brachyury. This is likely the result of the increased specification of definitive endoderm from the mesendoderm precursors. Lower levels of activin A treatment (10 and 30 ng/ml) maintain the expression of brachyury at later time points of differentiation relative to untreated control cultures.

FIGS. 15A-B are micrographs showing decreased parietal endoderm differentiation in response to treatment with activins. Regions of TM^(hi) parietal endoderm are found through the culture (A) when differentiated in serum alone, while differentiation to TM⁺ cells is scarce when activins are included (B) and overall intensity of TM immunoreactivity is lower.

FIGS. 16A-D are micrographs which show marker expression in response to treatment with activin A and activin B. hESCs were treated for four consecutive days with activin A and activin B and triple labeled with SOX17, AFP and TM antibodies. Panel A—SOX17; Panel B—AFP; Panel C—TM; and Panel D—Phase/DAPI. Notice the numerous SOX17 positive cells (A) associated with the complete absence of AFP (B) and TM (C) immunoreactivity.

FIG. 17 is a micrograph showing the appearance of definitive endoderm and visceral endoderm in vitro from hESCs. The regions of visceral endoderm are identified by AFP^(hi)/SOX17^(lo/−) while definitive endoderm displays the complete opposite profile, SOX17^(hi)/AFP^(lo/−). This field was selectively chosen due to the proximity of these two regions to each other. However, there are numerous times when SOX17^(hi)/AFP^(lo/−) regions are observed in absolute isolation from any regions of AFP^(hi) cells, suggesting the separate origination of the definitive endoderm cells from visceral endoderm cells.

FIG. 18 is a diagram depicting the TGFβ family of ligands and receptors. Factors activating AR Smads and BR Smads are useful in the production of definitive endoderm from human embryonic stem cells (see, J Cell Pyysiol. 187:265-76).

FIG. 19 is a bar chart showing the induction of SOX17 expression over time as a result of treatment with individual and combinations of TGFβ factors.

FIG. 20 is a bar chart showing the increase in SOX17⁺ cell number with time as a result of treatment with combinations of TGFβ factors.

FIG. 21 is a bar chart showing induction of SOX17 expression over time as a result of treatment with combinations of TGFβ factors.

FIG. 22 is a bar chart showing that activin A induces a dose-dependent increase in SOX17⁺ cell number.

FIG. 23 is a bar chart showing that addition of Wnt3a to activin A and activin B treated cultures increases SOX17 expression above the levels induced by activin A and activin B alone.

FIGS. 24A-C are bar charts showing differentiation to definitive endoderm is enhanced in low FBS conditions. Treatment of hESCs with activins A and B in media containing 2% FBS (2AA) yields a 2-3 times greater level of SOX17 expression as compared to the same treatment in 10% FBS media (10AA) (panel A). Induction of the definitive endoderm marker MIXL1 (panel B) is also affected in the same way and the suppression of AFP (visceral endoderm) (panel C) is greater in 2% FBS than in 10% FBS conditions.

FIGS. 25A-D are micrographs which show SOX17⁺ cells are dividing in culture. SOX17 immunoreactive cells are present at the differentiating edge of an hESC colony (C, D) and are labeled with proliferating cell nuclear antigen (PCNA) (panel B) yet are not co-labeled with OCT4 (panel C). In addition, clear mitotic figures can be seen by DAPI labeling of nuclei in both SOX17⁺ cells (arrows) as well as OCT4⁺, undifferentiated hESCs (arrowheads) (D).

FIG. 26 is a bar chart showing the relative expression level of CXCR4 in differentiating hESCs under various media conditions.

FIGS. 27A-D are bar charts that show how a panel of definitive endoderm markers share a very similar pattern of expression to CXCR4 across the same differentiation treatments displayed in FIG. 26.

FIGS. 28A-E are bar charts showing how markers for mesoderm (BRACHYURY, MOX1), ectoderm (SOX1, ZIC1) and visceral endoderm (SOX7) exhibit an inverse relationship to CXCR4 expression across the same treatments displayed in FIG. 26.

FIGS. 29A-F are micrographs that show the relative difference in SOX17 immunoreactive cells across three of the media conditions displayed in FIGS. 26-28.

FIGS. 30A-C are flow cytometry dot plots that demonstrate the increase in CXCR4⁺ cell number with increasing concentration of activin A added to the differentiation media.

FIGS. 31A-D are bar charts that show the CXCR4⁺ cells isolated from the high dose activin A treatment (A100-CX+) are even further enriched for definitive endoderm markers than the parent population (A100).

FIG. 32 is a bar chart showing gene expression from CXCR4⁺ and CXCR4⁻ cells isolated using fluorescence-activated cell sorting (FACS) as well as gene expression in the parent populations. This demonstrates that the CXCR4⁺ cells contain essentially all the CXCR4 gene expression present in each parent population and the CXCR4⁻ populations contain very little or no CXCR4 gene expression.

FIGS. 33A-D are bar charts that demonstrate the depletion of mesoderm (BRACHYURY, MOX1), ectoderm (ZIC1) and visceral endoderm (SOX7) gene expression in the CXCR4⁺ cells isolated from the high dose activin A treatment which is already suppressed in expression of these non-definitive endoderm markers.

FIGS. 34A-M are bar charts showing the expression patterns of marker genes that can be used to identify definitive endoderm cells. The expression analysis of definitive endoderm markers, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1 is shown in panels G-L, respectively. The expression analysis of previously described lineage marking genes, SOX17, SOX7, SOX17/SOX7, TM, ZIC1, and MOX1 is shown in panels A-F, respectively. Panel M shows the expression analysis of CXCR4. With respect to each of panels A-M, the column labeled hESC indicates gene expression from purified human embryonic stem cells; 2NF indicates cells treated with 2% FBS, no activin addition; 0.1A100 indicates cells treated with 0.1% FBS, 100 ng/ml activin A; 1A100 indicates cells treated with 1% FBS, 100 ng/ml activin A; and 2A100 indicates cells treated with 2% FBS, 100 ng/ml activin A.

FIGS. 35A-D show the in vivo differentiation of definitive endoderm cells that are transplanted under the kidney capsule of immunocompromised mice. Panels: A—hetatoxylin-eosin staining showing gut-tube-like structures; B—antibody immunoreactivity against hepatocyte specific antigen (liver); C—antibody immunoreactivity against villin (intestine); and D—antibody immunoreactivity against CDX2 (intestine).

FIGS. 36A-C are charts showing the normalized relative expression levels of markers for liver (albumin and PROX1) and lung (TITF1) tissues in cells contacted with Wnt3A at 20 ng/ml, FGF2 at 5 ng/ml or FGF2 at 100 ng/ml on days 5-10. DE refers to definitive endoderm. Panels: A—albumin, B—PROX1, and C—TITF1.

DETAILED DESCRIPTION

A crucial stage in early human development termed gastrulation occurs 2-3 weeks after fertilization. Gastrulation is extremely significant because it is at this time that the three primary germ layers are first specified and organized (Lu et al., 2001; Schoenwolf and Smith, 2000). The ectoderm is responsible for the eventual formation of the outer coverings of the body and the entire nervous system whereas the heart, blood, bone, skeletal muscle and other connective tissues are derived from the mesoderm. Definitive endoderm is defined as the germ layer that is responsible for formation of the entire gut tube which includes the esophagus, stomach and small and large intestines, and the organs which derive from the gut tube such as the lungs, liver, thymus, parathyroid and thyroid glands, gall bladder and pancreas (Grapin-Botton and Melton, 2000; Kimelman and Griffin, 2000; Tremblay et al., 2000; Wells and Melton, 1999; Wells and Melton, 2000). A very important distinction should be made between the definitive endoderm and the completely separate lineage of cells termed primitive endoderm. The primitive endoderm is primarily responsible for formation of extra-embryonic tissues, mainly the parietal and visceral endoderm portions of the placental yolk sac and the extracellular matrix material of Reichert's membrane.

During gastrulation, the process of definitive endoderm formation begins with a cellular migration event in which mesendoderm cells (cells competent to form mesoderm or endoderm) migrate through a structure called the primitive streak. Definitive endoderm is derived from cells, which migrate through the anterior portion of the streak and through the node (a specialized structure at the anterior-most region of the streak). As migration occurs, definitive endoderm populates first the most anterior gut tube and culminates with the formation of the posterior end of the gut tube.

In vivo analyses of the formation of definitive endoderm, such as the studies in Zebrafish and Xenopus by Conlon et al., 1994; Feldman et al., 1998; Zhou et al., 1993; Aoki et al., 2002; Dougan et al., 2003; Tremblay et al., 2000; Vincent et al., 2003; Alexander et al., 1999; Alexander and Stainier, 1999; Kikuchi et al., 2001; Hudson et al., 1997 and in mouse by Kanai-Azuma et al., 2002 lay a foundation for how one might attempt to approach the development of a specific germ layer cell type in the culture dish using human embryonic stem cells. There are two aspects associated with in vitro ESC culture that pose major obstacles in the attempt to recapitulate development in the culture dish. First, organized germ layer or organ structures are not produced. The majority of germ layer and organ specific genetic markers will be expressed in a heterogeneous fashion in the differentiating HESC culture system. Therefore it is difficult to evaluate formation of a specific tissue or cell type due to this lack of organ specific boundaries. Almost all genes expressed in one cell type within a particular germ layer or tissue type are expressed in other cells of different germ layer or tissue types as well. Without specific boundaries there is considerably less means to assign gene expression specificity with a small sample of 1-3 genes. Therefore one must examine considerably more genes, some of which should be present as well as some that should not be expressed in the particular cell type of the organ or tissue of interest. Second, the timing of gene expression patterns is crucial to movement down a specific developmental pathway.

To further complicate matters, it should be noted that stem cell differentiation in vitro is rather asynchronous, likely considerably more so than in vivo. As such, one group of cells may be expressing genes associated with gastrulation, while another group may be starting final differentiation. Furthermore, manipulation of HESC monolayers or embryoid bodies (EBs) with or without exogenous factor application may result in profound differences with respect to overall gene expression pattern and state of differentiation. For these reasons, the application of exogenous factors must be timed according to gene expression patterns within a heterogeneous cell mixture in order to efficiently move the culture down a specific differentiation pathway. It is also beneficial to consider the morphological association of the cells in the culture vessel. The ability to uniformly influence hESCs when formed into so called embryoid bodies may be less optimal than hESCs grown and differentiated as monolayers and or HESC colonies in the culture vessel.

As an effective way to deal with the above-mentioned problems, some embodiments of the present invention contemplate combining a method for differentiating cells with a method for the enrichment, isolation and/or purification and identification of intermediate cell types in the differentiation pathway.

DEFINITIONS

Certain terms and phrases as used throughout this application have the meanings provided as follows:

As used herein, “embryonic” refers to a range of developmental stages of an organism beginning with a single zygote and ending with a multicellular structure that no longer comprises pluripotent or totipotent cells other than developed gametic cells. In addition to embryos derived by gamete fusion, the term “embryonic” refers to embryos derived by somatic cell nuclear transfer.

As used herein, “multipotent” or “multipotent cell” refers to a cell type that can give rise to a limited number of other particular cell types. Multipotent cells are committed to one or more, but not all, embryonic and/or extraembryonic cell fates. Thus, in contrast to pluripotent cells, multipotent cells cannot give rise to each of the three embryonic cell lineages as well as extraembryonic cells.

In some embodiments, hESCs can be derived from a “preimplantation embryo.” As used herein, “preimplantation embryo” refers to an embryo between the stages of fertilization and implantation. Implantation generally takes place 7-8 days after fertilization. However, implantation may take place about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14 or greater than about 14 days after fertilization. In some embodiments, a preimplantation embryo has not progressed beyond the blastocyst stage.

As used herein, “expression” refers to the production of a material or substance as well as the level or amount of production of a material or substance. Thus, determining the expression of a specific marker refers to detecting either the relative or absolute amount of the marker that is expressed or simply detecting the presence or absence of the marker.

As used herein, “marker” refers to any molecule that can be observed or detected. For example, a marker can include, but is not limited to, a nucleic acid, such as a transcript of a specific gene, a polypeptide product of a gene, a non-gene product polypeptide, a glycoprotein, a carbohydrate, a glycolipid, a lipid, a lipoprotein or a small molecule (for example, molecules having a molecular weight of less than 10,000 amu)

When used in connection with cell cultures and/or cell populations, the term “portion” means any non-zero amount of the cell culture or cell population, which ranges from a single cell to the entirety of the cell culture or cells population.

With respect to cells in cell cultures or in cell populations, the phrase “substantially free of” means that the specified cell type of which the cell culture or cell population is free, is present in an amount of less than about 5% of the total number of cells present in the cell culture or cell population.

“Stringency” of hybridization reactions is readily determinable by those skilled in the art, and generally is an empirical calculation based upon oligonucleotide length and composition, washing temperature, sand salt concentration. In general, longer oligonucleotides may anneal at relatively high temperatures, while shorter oligonucleotides generally anneal at lower temperatures. Hybridization generally depends on the ability of denatured nucleic acid to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the oligonucleotide and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).

“Stringent conditions” or “high stringency conditions,” as used herein, are identified by those that: (1) employ low ionic strength and high temperature for washing, for example 0.015M sodium chloride/0.0015M sodium citrate/0.1% SDS at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C., or (3) for example, employ 50% formamide, 5×SSC (0.75M NaCl, 0.075 M sodium citrate) 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/mL) 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.

“Moderately stringent conditions” may be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent that those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

As used herein, the term “label” refers to, for example, radioactive, fluorescent, biological or enzymatic tags or labels of standard use in the art. A label can be conjugated, or otherwise bound, to nucleic acids, polypeptides, such as antibodies, or small molecules. For example, oligonucleotides of the present invention can be labeled subsequent to synthesis, by incorporating biotinylated dNTPs or rNTP, or some similar means (e.g., photo-cross-linking a psoralen derivative of biotin to RNAs), followed by addition of labeled streptavidin (e.g., phycoerythrin-conjugated streptavidin) or the equivalent. Alternatively, when fluorescently-labeled oligonucleotide probes are used, fluorescein, lissamine, phycoerythirin, rhodamine (Perkin Elmer Cetus), Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, FluorX (Amersham) and others, can be attached to nucleic acids. Non-limiting examples of detectable labels that may be conjugated to polypeptides such as antibodies include but are not limited to radioactive labels, such as ³H, ¹¹C, ¹⁴C, ¹⁸F, ³²P, ³⁵S, ⁶⁴Cu, ⁷⁶Br, ⁸⁶Y, ⁹⁹Tc, ¹¹¹In, ¹²³I, ¹²⁵I, or ¹⁷⁷Lu, enzymes, such as horseradish peroxidase, fluorophores, chromophores, chemiluminescent agents, chelating complexes, dyes, colloidal gold or latex particles.

Definitive Endoderm Cells and Processes Related Thereto

Embodiments described herein relate to the production, identification, and isolation and/or enrichment of definitive endoderm cells in culture by differentiating pluripotent cells, such as stem cells. As described above, definitive endoderm cells do not differentiate into tissues produced from ectoderm or mesoderm, but rather, differentiate into the gut tube as well as organs that are derived from the gut tube. In certain preferred embodiments, the definitive endoderm cells are derived from hESCs. Such processes can provide the basis for efficient production of human endodermal derived tissues such as pancreas, liver, lung, stomach, intestine, thyroid and thymus. For example, production of definitive endoderm may be the first step in differentiation of a stem cell to a functional insulin-producing β-cell. To obtain useful quantities of insulin-producing β-cells, high efficiency of differentiation is desirable for each of the differentiation steps that occur prior to reaching the pancreatic islet/β-cell fate. Since differentiation of stem cells to definitive endoderm cells represents an early step towards the production of functional pancreatic islet/β-cells (as shown in FIG. 1), high efficiency of differentiation at this step is particularly desirable.

In view of the desirability of efficient differentiation of pluripotent cells to definitive endoderm cells, some aspects of the differentiation processes described herein relate to in vitro methodology that results in approximately 50-80% conversion of pluripotent cells to definitive endoderm cells. Typically, such methods encompass the application of culture and growth factor conditions in a defined and temporally specified fashion. Further enrichment of the cell population for definitive endoderm cells can be achieved by isolation and/or purification of the definitive endoderm cells from other cells in the population by using a reagent that specifically binds to definitive endoderm cells. As such, some embodiments described herein relate to definitive endoderm cells as well as methods for producing and isolating and/or purifying such cells.

In order to determine the amount of definitive endoderm cells in a cell culture or cell population, a method of distinguishing this cell type from the other cells in the culture or in the population is desirable. Accordingly, certain embodiments described herein relate to cell markers whose presence, absence and/or relative expression levels are specific for definitive endoderm and methods for detecting and determining the expression of such markers.

In some embodiments described herein, the presence, absence and/or level of expression of a marker is determined by quantitative PCR (Q-PCR). For example, the amount of transcript produced by certain genetic markers, such as one or more markers selected from Table 3 is determined by quantitative Q-PCR. In other embodiments, immunohistochemistry is used to detect the proteins expressed by the above-mentioned genes. In a preferred embodiment, immunohistochemistry is used to detect one or more cell surface markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. In still other embodiments, Q-PCR and immunohistochemical techniques are both used to identify and determine the amount or relative proportions of markers, such as those selected from Table 3.

By using methods, such as those described above, to determine the expression of one or more appropriate markers, it is possible to identify definitive endoderm cells, as well as determine the proportion of definitive endoderm cells in a cell culture or cell population. For example, in some embodiments of the present invention, the definitive endoderm cells or cell populations that are produced express one or more markers selected from Table 3 at a level of about 2 orders of magnitude greater than non-definitive endoderm cell types or cell populations. In certain embodiments, the non-definitive endoderm cell types consist only of hESCs. In other embodiments, the definitive endoderm cells or cell populations that are produced express one or more markers selected from Table 3 at a level of more than 2 orders of magnitude greater than non-definitive endoderm cell types or cell populations. In particular embodiments, the non-definitive endoderm cell types consist only of hESCs. In still other embodiments, the definitive endoderm cells or cell populations that are produced express one or more of the markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 at a level of about 2 or more than 2 orders of magnitude greater than non-definitive endoderm cell types or cell populations. In certain embodiments, the non-definitive endoderm cell types consist only of hESCs. In some embodiments described herein, definitive endoderm cells do not substantially express PDX1.

Embodiments described herein also relate to definitive endoderm compositions. For example, some embodiments relate to cell cultures comprising definitive endoderm, whereas others relate to cell populations enriched in definitive endoderm cells. Some preferred embodiments relate to cell cultures which comprise definitive endoderm cells, wherein at least about 50-80% of the cells in culture are definitive endoderm cells. An especially preferred embodiment relates to cells cultures comprising human cells, wherein at least about 50-80% of the human cells in culture are definitive endoderm cells. Because the efficiency of the differentiation procedure can be adjusted by modifying certain parameters, which include but are not limited to, cell growth conditions, growth factor concentrations and the timing of culture steps, the differentiation procedures described herein can result in about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or greater than about 95% conversion of pluripotent cells to definitive endoderm. In other preferred embodiments, conversion of a pluripotent cell population, such as a stem cell population, to substantially pure definitive endoderm cell population is contemplated.

The compositions and methods described herein have several useful features. For example, the cell cultures and cell populations comprising definitive endoderm as well as the methods for producing such cell cultures and cell populations are useful for modeling the early stages of human development. Furthermore, the compositions and methods described herein can also serve for therapeutic intervention in disease states, such as diabetes mellitus. For example, since definitive endoderm serves as the source for only a limited number of tissues, it can be used in the development of pure tissue or cell types.

Production of Definitive Endoderm from Pluripotent Cells

Processes for differentiating pluripotent cells to produce cell cultures and enriched cell populations comprising definitive endoderm is described below and in U.S. patent Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004, the disclosure of which is incorporated herein by reference in its entirety. In some of these processes, the pluripotent cells used as starting material are stem cells. In certain processes, definitive endoderm cell cultures and enriched cell populations comprising definitive endoderm cells are produced from embryonic stem cells. A preferred method for deriving definitive endoderm cells utilizes human embryonic stem cells as the starting material for definitive endoderm production. Such pluripotent cells can be cells that originate from the morula, embryonic inner cell mass or those obtained from embryonic gonadal ridges. Human embryonic stem cells can be maintained in culture in a pluripotent state without substantial differentiation using methods that are known in the art. Such methods are described, for example, in U.S. Pat. Nos. 5,453,357, 5,670,372, 5,690,926 5,843,780, 6,200,806 and 6,251,671 the disclosures of which are incorporated herein by reference in their entireties.

In some processes for producing definitive endoderm cells, hESCs are maintained on a feeder layer. In such processes, any feeder layer which allows hESCs to be maintained in a pluripotent state can be used. One commonly used feeder layer for the cultivation of human embryonic stem cells is a layer of mouse fibroblasts. More recently, human fibroblast feeder layers have been developed for use in the cultivation of hESCs (see US Patent Application No. 2002/0072117, the disclosure of which is incorporated herein by reference in its entirety). Alternative processes for producing definitive endoderm permit the maintenance of pluripotent HESC without the use of a feeder layer. Methods of maintaining pluripotent hESCs under feeder-free conditions have been described in US Patent Application No. 2003/0175956, the disclosure of which is incorporated herein by reference in its entirety.

The human embryonic stem cells used herein can be maintained in culture either with or without serum. In some embryonic stem cell maintenance procedures, serum replacement is used. In others, serum free culture techniques, such as those described in US Patent Application No. 2003/0190748, the disclosure of which is incorporated herein by reference in its entirety, are used.

Stem cells are maintained in culture in a pluripotent state by routine passage until it is desired that they be differentiated into definitive endoderm. In some processes, differentiation to definitive endoderm is achieved by providing to the stem cell culture a growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation to definitive endoderm. Growth factors of the TGFβ superfamily which are useful for the production of definitive endoderm are selected from the Nodal/Activin or BMP subgroups. In some preferred differentiation processes, the growth factor is selected from the group consisting of Nodal, activin A, activin B and BMP4. Additionally, the growth factor Wnt3a and other Wnt family members are useful for the production of definitive endoderm cells. In certain differentiation processes, combinations of any of the above-mentioned growth factors can be used.

With respect to some of the processes for the differentiation of pluripotent stem cells to definitive endoderm cells, the above-mentioned growth factors are provided to the cells so that the growth factors are present in the cultures at concentrations sufficient to promote differentiation of at least a portion of the stem cells to definitive endoderm cells. In some processes, the above-mentioned growth factors are present in the cell culture at a concentration of at least about 5 ng/ml, at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, at least about 1000 ng/ml, at least about 2000 ng/ml, at least about 3000 ng/ml, at least about 4000 ng/ml, at least about 5000 ng/ml or more than about 5000 ng/ml.

In certain processes for the differentiation of pluripotent stem cells to definitive endoderm cells, the above-mentioned growth factors are removed from the cell culture subsequent to their addition. For example, the growth factors can be removed within about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days or about ten days after their addition. In a preferred processes, the growth factors are removed about four days after their addition.

Cultures of definitive endoderm cells can be grown in medium containing reduced serum or no serum. Under certain culture conditions, serum concentrations can range from about 0.05% v/v to about 20% v/v. For example, in some differentiation processes, the serum concentration of the medium can be less than about 0.05% (v/v), less than about 0.1% (v/v), less than about 0.2% (v/v), less than about 0.3% (v/v), less than about 0.4% (v/v), less than about 0.5% (v/v), less than about 0.6% (v/v), less than about 0.7% (v/v), less than about 0.8% (v/v), less than about 0.9% (v/v), less than about 1% (v/v), less than about 2% (v/v), less than about 3% (v/v), less than about 4% (v/v), less than about 5% (v/v), less than about 6% (v/v), less than about 7% (v/v), less than about 8% (v/v), less than about 9% (v/v), less than about 10% (v/v), less than about 15% (v/v) or less than about 20% (v/v). In some processes, definitive endoderm cells are grown without serum or with serum replacement. In still other processes, definitive endoderm cells are grown in the presence of B27. In such processes, the concentration of B27 supplement can range from about 0.1% v/v to about 20% v/v.

Monitoring the Differentiation of Pluripotent Cells to Definitive Endoderm

The progression of the HESC culture to definitive endoderm can be monitored by determining the expression of markers characteristic of definitive endoderm. In some processes, the expression of certain markers is determined by detecting the presence or absence of the marker. Alternatively, the expression of certain markers can be determined by measuring the level at which the marker is present in the cells of the cell culture or cell population. In such processes, the measurement of marker expression can be qualitative or quantitative. One method of quantitating the expression of markers that are produced by marker genes is through the use of quantitative PCR (Q-PCR). Methods of performing Q-PCR are well known in the art. Other methods which are known in the art can also be used to quantitate marker gene expression. For example, the expression of a marker gene product can be detected by using antibodies specific for the marker gene product of interest. In certain processes, the expression of marker genes characteristic of definitive endoderm as well as the lack of significant expression of marker genes characteristic of hESCs and other cell types is determined.

As described further in the Examples below, a reliable marker of definitive endoderm is the SOX17 gene. As such, the definitive endoderm cells produced by the processes described herein express the SOX17 marker gene, thereby producing the SOX17 gene product. Other markers of definitive endoderm are markers selected from Table 3. Since definitive endoderm cells express the SOX17 marker gene at a level higher than that of the SOX7 marker gene, which is characteristic of primitive and visceral endoderm (see Table 1), in some processes, the expression of both SOX17 and SOX7 is monitored. In other processes, expression of the both the SOX17 marker gene and the OCT4 marker gene, which is characteristic of hESCs, is monitored. Additionally, because definitive endoderm cells express the SOX17 marker gene at a level higher than that of the AFP, SPARC or Thrombomodulin (TM) marker genes, the expression of these genes can also be monitored.

Another marker of definitive endoderm is the CXCR4 gene. The CXCR4 gene encodes a cell surface chemokine receptor whose ligand is the chemoattractant SDF-1. The principal roles of the CXCR4 receptor-bearing cells in the adult are believed to be the migration of hematopoetic cells to the bone marrow, lymphocyte trafficking and the differentiation of various B cell and macrophage blood cell lineages [Kim, C., and Broxmeyer, H. J. Leukocyte Biol. 65, 6-15 (1999)]. The CXCR4 receptor also functions as a coreceptor for the entry of HIV-1 into T-cells [Feng, Y., et al. Science, 272, 872-877 (1996)]. In an extensive series of studies carried out by [McGrath, K. E. et al. Dev. Biology 213, 442-456 (1999)], the expression of the chernokine receptor CXCR4 and its unique ligand, SDF-1 [Kim, C., and Broxmyer, H., J. Leukocyte Biol. 65, 6-15 (1999)], were delineated during early development and adult life in the mouse. The CXCR4/SDF1 interaction in development became apparent when it was demonstrated that if either gene was disrupted in transgenic mice [Nagasawa et al. Nature, 382, 635-638 (1996)], Ma, Q., et al Immunity, 10, 463-471 (1999)] it resulted in late embryonic lethality. McGrath et al. demonstrated that CXCR4 is the most abundant chemokine receptor messenger RNA detected during early gastrulating embryos (E7.5) using a combination of RNase protection and in situ hybridization methodologies. In the gastrulating embryo, CXCR4/SDF-1 signaling appears to be mainly involved in inducing migration of primitive-streak germlayer cells and is expressed on definitive endoderm, mesoderm and extraembryonic mesoderm present at this time. In E7.2-7.8 mouse embryos, CXCR4 and alpha-fetoprotein are mutually exclusive indicating a lack of expression in visceral endoderm [McGrath, K. E. et al. Dev. Biology 213, 442-456 (1999)].

Since definitive endoderm cells produced by differentiating pluripotent cells express the CXCR4 marker gene, expression of CXCR4 can be monitored in order to track the production of definitive endoderm cells. Additionally, definitive endoderm cells produced by the methods described herein express other markers of definitive endoderm including, but not limited to, one or more markers selected from Table 3. Since definitive endoderm cells express the CXCR4 marker gene at a level higher than that of the SOX7 marker gene, the expression of both CXCR4 and SOX7 can be monitored. In other processes, expression of both the CXCR4 marker gene and the OCT4 marker gene, is monitored. Additionally, because definitive endoderm cells express the CXCR4 marker gene at a level higher than that of the AFP, SPARC or Thrombomodulin (TM) marker genes, the expression of these genes can also be monitored.

It will be appreciated that in some embodiments described herein, the expression of one or more markers selected from Table 3 in definitive endoderm cells is increased as compared to the expression of one or more markers selected from the group consisting of OCT4, SPARC, AFP, TM and SOX7 in definitive endoderm cells. In preferred embodiments, the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 in definitive endoderm cells is increased as compared to the expression of one or more markers selected from the group consisting of OCT4, SPARC, AFP, TM and SOX7 in definitive endoderm cells.

It will be appreciated that expression of CXCR4 in endodermal cells does not preclude the expression of SOX17. Furthermore, the expression of one or more markers selected from Table 3 in definitive endoderm does not preclude the expression of other markers selected from Table 3. As such, definitive endoderm cells produced by the processes described herein will substantially express SOX17, CXCR4 and one or more other markers selected from Table 3, but will not substantially express AFP, TM, SPARC or PDX1.

It will be appreciated that the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is induced over a range of different levels in definitive endoderm cells depending on the differentiation conditions. As such, in some embodiments described herein, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 in definitive endoderm cells or cell populations is at least about 2-fold higher to at least about 10,000-fold higher than the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 in non-definitive endoderm cells or cell populations, for example pluripotent stem cells. In other embodiments, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 in definitive endoderm cells or cell populations is at least about 4-fold higher, at least about 6-fold higher, at least about 8-fold higher, at least about 10-fold higher, at least about 15-fold higher, at least about 20-fold higher, at least about 40-fold higher, at least about 80-fold higher, at least about 100-fold higher, at least about 150-fold higher, at least about 200-fold higher, at least about 500-fold higher, at least about 750-fold higher, at least about 1000-fold higher, at least about 2500-fold higher, at least about 5000-fold higher, at least about 7500-fold higher or at least about 10,000-fold higher than the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 in non-definitive endoderm cells or cell populations, for example pluripotent stem cells. In some embodiments, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 in definitive endoderm cells or cell populations is infinitely higher than the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 in non-definitive endoderm cells or cell populations, for example pluripotent stem cells. In preferred embodiments of the above-described processes, the expression of one or more markers selected from Table 3, including one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192, in definitive endoderm cells or cell populations is increased as compared to the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 in non-definitive endoderm cells or cell populations.

Additionally, it will be appreciated that there is a range of differences between the expression level of SOX17, CXCR4 and/or one or more other markers selected from Table 3 and the expression levels of the OCT4, SPARC, AFP, TM and/or SOX7 markers in definitive endoderm cells. As such, in some embodiments described herein, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is at least about 2-fold higher to at least about 10,000-fold higher than the expression of OCT4, SPARC, AFP, TM and/or SOX7 markers. In other embodiments, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is at least about 4-fold higher, at least about 6-fold higher, at least about 8-fold higher, at least about 10-fold higher, at least about 15-fold higher, at least about 20-fold higher, at least about 40-fold higher, at least about 80-fold higher, at least about 100-fold higher, at least about 150-fold higher, at least about 200-fold higher, at least about 500-fold higher, at least about 750-fold higher, at least about 1000-fold higher, at least about 2500-fold higher, at least about 5000-fold higher, at least about 7500-fold higher or at least about 10,000-fold higher than the expression of OCT4, SPARC, AFP, TM and/or SOX7 markers. In some embodiments, OCT4, SPARC, AFP, TM and/or SOX7 markers are not significantly expressed in definitive endoderm cells.

Enrichment, Isolation and/or Purification of Definitive Endoderm

With respect to aspects of the present invention, definitive endoderm cells can be enriched, isolated and/or purified by contacting a cell population that includes definitive endoderm cells with a reagent that binds to a marker, which is expressed in definitive endoderm cells but not substantially expressed in one or more non-definitive endoderm cell types, and separating cells bound by the reagent from cells that are not bound by the reagent.

In some embodiments, the marker can be any marker that is expressed in definitive endoderm cells but not substantially expressed in one or more non-definitive endoderm cell types. Such markers include, but are not limited to, markers that are more highly expressed in definitive endoderm cells than hESCs, mesoderm cells, ectoderm cells, and/or extra-embryonic endoderm cells. Non-limiting examples of useful markers expressed in definitive endoderm cells, but not substantially expressed in one or more non-definitive endoderm cell types, are provided in Table 3. Certain preferred markers include one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 (highly expressed markers described in Table 4). Other preferred markers include one or more markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1 (cell surface markers described in Table 5).

In some embodiments, the reagent can be any type of affinity tag that is specific, or at least partially specific, for definitive endoderm cells, such as antibodies, ligands or other binding agents that are specific, or at least partially specific, to a marker molecule, such as a polypeptide, that is present in definitive endoderm cells but which is not substantially present in other cell types that are found in a cell culture produced by the methods described herein.

Reagents that bind to definitive endoderm associated markers described herein can form reagent-cell complexes with definitive endoderm cells. In some embodiments, subsequent to providing a cell population with a reagent that binds to a marker, unbound reagent can be removed from the composition by washing, stirring, and/or filtering. One example of reagent-cell complex is an antibody-antigen complex. In preferred embodiments of such complexes, the antigen marker can be localized to the cell surface. Another example of a reagent-cell complex is a receptor-ligand complex, wherein the receptor is expressed in definitive endoderm cells but not substantially expressed in one or more non-definitive endoderm cell types. In preferred embodiments, the ligand can bind to the receptor-binding domain without appreciably affecting the receptor activity. In still other preferred embodiments, the ligand is attached to another molecule so as to facilitate easy manipulation of the reagent cell complex. For example, in cases where the ligand is a small molecule, the ligand can be linked to a macromolecule, such as a carbohydrate, a protein or a synthetic polymer. In some embodiments, the macromolecules can be coupled to, for example, labels, particles, such as magnetic particles, or surfaces, such as a solid support. Table 5 lists several polypeptides which are localized at the cell surface, including receptors, which are expressed in definitive endoderm cells but not substantially expressed in one or more non-definitive endoderm cell types.

In some embodiments of the present invention, an antibody is prepared for use as an affinity tag for the enrichment, isolation and/or purification of definitive endoderm cells. Methods for making antibodies, for example, the methods described in Kohler, G., and C. Milstein. 1975. Continuous cultures of fused cells secreting antibody of predefined specificity. Nature 256:495-497, the disclosure of which is incorporated herein by reference in its entirety, are well known in the art. Additionally, antibodies and fragments can be made by other standardized methods (See, for example, E. Harlow et al., Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1988). The isolation, identification, and molecular construction of antibodies has been developed to such an extent that the choices are almost inexhaustible. Therefore, examples of methods for making various antibodies, antibody fragments and/or antibody complexes will be provided with the understanding that this only represents a sampling of what is known to those of ordinary skill in the art.

Antibodies can be whole immunoglobulin (IgG) of any class, e.g., IgG, IgM, IgA, IgD, IgE, chimeric antibodies or hybrid antibodies with dual or multiple antigen or epitope specificities, or fragments, such as F(ab′)₂, Fab′, Fab and the like, including hybrid fragments. It will be understood that any immunoglobulin or any natural, synthetic, or genetically engineered protein that acts like an antibody by binding to marker of definitive endoderm can be used.

Preparations of polyclonal antibodies can be made using standard methods which are well known in the art. Antibodies can include antiserum preparations from a variety of commonly used animals, e.g., goats, primates, donkeys, swine, rabbits, horses, hens, guinea pigs, rats, or mice, and even human antisera after appropriate selection and purification. Animal antisera are raised by inoculating the animals with immunogenic epitopes from one or more recombinantly-expressed polypeptide markers selected from Table 3. The animals are then bled and the serum or an immunoglobulin-containing serum fraction is recovered.

Hybridoma-derived monoclonal antibodies (human, monkey, rat, mouse, or the like) are also suitable for use in the present invention. Monoclonal antibodies typically display a high degree of specificity. Such antibodies are readily prepared by conventional procedures for the immunization of mammals with preparations such as, the immunogenic epitopes of one or more markers selected from Table 3, fusion of immune lymph or spleen cells with an immortal myeloma cell line, and isolation of specific hybridoma clones. In addition to the foregoing procedure, alternate method of preparing monoclonal antibodies are also useful. Such methods can include interspecies fusions and genetic engineering manipulations of hypervariable regions.

In one embodiment of the present invention, the antibody is a single chain Fv region. Antibody molecules have two generally recognized regions, in each of the heavy and light chains. These regions are the so-called “variable” region which is responsible for binding to the specific antigen in question, and the so-called “constant” region which is responsible for biological effector responses such as complement binding, binding to neutrophils and macrophages, etc. The constant regions have been separated from the antibody molecule and variable binding regions have been obtained. Fragments containing the variable region, but lacking the constant region, are sufficient for antigen binding.

The variable regions of an antibody are composed of a light chain and a heavy chain. Light and heavy chain variable regions have been cloned and expressed in foreign hosts, while maintaining their binding ability. Therefore, it is possible to generate a single chain structure from the multiple chain aggregate (the antibody), such that the single chain structure will retain the three-dimensional architecture of the multiple chain aggregate.

In some embodiments, single polypeptide chain Fv fragments having the characteristic binding ability of multi-chain variable regions of antibody molecules can be used to bind one or markers selected from Table 3. Such single chain fragments can be produced, for example, following the methods described in U.S. Pat. No. 5,260,203, the disclosure of which is incorporated herein by reference in its entirety, using a computer based system and method to determine chemical structures. These chemical structures are used for converting two naturally aggregated but chemically separated light and heavy polypeptide chains from an antibody variable region into a single polypeptide chain which will fold into a three dimensional structure very similar to the original structure of the two polypeptide chains. The two regions may be linked using an amino acid sequence as a bridge.

The single polypeptide chain obtained from this method can then be used to prepare a genetic sequence that encodes it. The genetic sequence can then be replicated in appropriate hosts, further linked to control regions, and transformed into expression hosts, where it is expressed. The resulting single polypeptide chain binding protein, upon refolding, has the binding characteristics of the aggregate of the original two (heavy and light) polypeptide chains of the variable region of the antibody.

In a further embodiment, the antibodies used herein can multivalent forms of single-chain antigen-binding proteins. Multivalent forms of single-chain antigen-binding proteins have additional utility beyond that of the monovalent single-chain antigen-binding proteins. In particular, a multivalent antigen-binding protein has more than one antigen-binding site which results in an enhanced binding affinity. The multivalent antibodies can be produced using the method disclosed in U.S. Pat. No. 5,869,620, the disclosure of which is incorporated herein by reference in its entirety. The method involves producing a multivalent antigen-binding protein by linking at least two single-chain molecules, each single chain molecule having two binding portions of the variable region of an antibody heavy or light chain linked into a single chain protein. In this way the antibodies can have binding sites for different parts of an antigen or have binding sites for multiple antigens.

In another embodiment, the antibody can be an oligomer. The oligomer is produced as in WO98/18943, the disclosure of which is incorporated herein by reference in its entirety, by first isolating a specific ligand from a phage-display library. Oligomers overcome the problem of the isolation of mostly low affinity ligands from these libraries, by oligomerizing the low-affinity ligands to produce high affinity oligomers. The oligomers are constructed by producing a fusion protein with the ligand fused to a semi-rigid hinge and a coiled coil domain from, for example, Cartilage Oligomeric Matrix Protein (COMP). When the fusion protein is expressed in a host cell, it self assembles into oligomers.

Preferably, the oligomers are peptabodies (Terskikh et al., Biochemistry 94:1663-1668 (1997)). Peptabodies can be exemplified as IgM antibodies which are pentameric with each binding site having low-affinity binding, but able to bind in a high affinity manner as a complex. Peptabodies are made using phage-display random peptide libraries. A short peptide ligand from the library is fused via a semi-rigid hinge at the N-terminus of a COMP pentamerization domain. The fusion protein is expressed in bacteria where it assembles into a pentameric antibody which shows high affinity for its target. Depending on the affinity of the ligand, an antibody with very high affinity can be produced.

Several generally applicable methods for using antibodies in affinity-based isolation and purification methods are known in the art. Such methods can be implemented for use with the antibodies and cells described herein. In preferred embodiments, an antibody which binds to one of the cell surface markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1 is attached to a magnetic bead then allowed to bind to definitive endoderm cells in a cell culture which has been enzymatically treated to reduce intercellular and substrate adhesion, to form reagent-cell complexes. The reagent-cell complexes are then exposed to a movable magnetic field which is used to separate reagent-bound definitive endoderm cells from unbound cells. Once the definitive endoderm cells are physically separated from other cells in culture, the antibody binding is disrupted and the cells are replated in appropriate tissue culture medium, thereby producing a population of cells enriched for definitive endoderm.

Other methods of enrichment, isolation and/or purification using antibodies to form antibody-cell complexes are contemplated. For example, in some embodiments, a primary antibody which binds to a marker expressed in definitive endoderm cells, but not substantially expressed in one or more non-definitive endoderm cell types, is incubated with a definitive endoderm-containing cell culture that has been treated to reduce intercellular and substrate adhesion, to form antibody-cell complexes. In preferred embodiments, the primary antibody comprises one or more antibodies that bind to a cell surface polypeptide selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA. The cells are then washed, centrifuged and resuspended. The cell suspension is then incubated with a secondary antibody, such as an FITC-conjugated antibody that is capable of binding to the primary antibody of the reagent-cell complex. The cells are then washed, centrifuged and resuspended in buffer. The cell suspension is then analyzed and sorted using a fluorescence activated cell sorter (FACS). Antibody-bound cells are collected separately from cells that are not bound by the antibody, thereby resulting in the isolation of such cell types. If desired, the enriched cell compositions can be further purified by using an alternate affinity-based method or by additional rounds of sorting using the same or different markers that are specific for definitive endoderm.

Additional methods of enrichment, isolation and/or purification related to using a ligand-based reagent to form ligand-cell complexes. For example, ligand-cell complexes can include a ligand-based reagent and receptor that is expressed on definitive endoderm but not substantially expressed in one or more non-definitive endoderm cell types. In such embodiments, ligand-based reagents are used as an affinity tag for the enrichment, isolation and/or purification of definitive endoderm cells. By way of example, the chemokine SDF-1, which is a ligand for CXCR4, or other molecules based on SDF-1 is a useful reagent in the enrichment, isolation and/or purification methods described herein. Likewise, SDF-1 fragments, SDF-1 fusions or SDF-1 mimetics that retain the ability to form reagent-cell complexes are useful in the enrichment, isolation and/or purification methods described herein. In some embodiments, the ligand is a ligand that binds to one of the cell surface markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. In preferred embodiments, a ligand that binds to one of the cell surface markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1 is attached directly to a macromolecule or a solid support. In other preferred embodiments, a ligand that binds to one of the cell surface markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1 is attached via a linker to a macromolecule or a solid support. In such embodiments, non-bound cells can be removed from the ligand-cell complexes by washing.

Alternatively, in some embodiments of the processes described herein, definitive endoderm cells are fluorescently labeled by recombinant expression of a fluorescent polypeptide or fragment thereof in definitive endoderm cells. For example, a nucleic acid encoding green fluorescent protein (GFP) or a nucleic acid encoding a different expressible fluorescent marker gene is used to label definitive endoderm cells. Various fluorescent marker genes are known in the art, such as luciferase, enhanced green fluorescent protein (EGFP), DS-Red monomer fluorescent protein (Clontech) and others. Any such markers can be used with the enrichment, isolation and/or purification methods described herein. For example, in some embodiments, at least one copy of a nucleic acid encoding GFP or a biologically active fragment thereof is introduced into a pluripotent cell, preferably a human embryonic stem cell, downstream of the promoter of any of the marker genes described herein that are expressed in definitive endoderm cells, but not substantially expressed in one or more non-definitive endoderm cell types, including those listed in Table 3, such that the expression of the GFP gene product or biologically active fragment thereof is under control of the marker gene's promoter. In some embodiments, the entire coding region of the nucleic acid, which encodes the marker, is replaced by a nucleic acid encoding GFP or a biologically active fragment thereof. In other embodiments, the nucleic acid encoding GFP or a biologically active fragment thereof is fused in frame with at least a portion of the nucleic acid encoding the marker, thereby generating a fusion protein. In such embodiments, the fusion protein retains a fluorescent activity similar to GFP.

The fluorescently-tagged cells produced by the above-described methods are then differentiated to definitive endoderm cells using the differentiation methods described herein. Because definitive endoderm cells express the fluorescent marker gene, whereas non-endoderm cells do not, these two cell types can be separated. In some embodiments, cell suspensions comprising a mixture of fluorescently-labeled definitive endoderm cells and unlabeled non-definitive endoderm cells are sorted using a FACS. Definitive endoderm cells are collected separately from non-definitive endoderm cells, thereby resulting in the isolation of such cell types. If desired, the isolated cell compositions can be further purified by additional rounds of sorting using the same or different markers that are specific for definitive endoderm cells.

Using the methods and compositions described herein, enriched, isolated and/or purified populations of definitive endoderm cells and/or tissues can be produced in vitro from HESC cultures or cell populations which have undergone differentiation for from about 1 hour to greater than about 144 hours. In some embodiments, the cells undergo random differentiation. In a preferred embodiment, however, the cells are directed to differentiate primarily into definitive endoderm cells. Some preferred enrichment, isolation and/or purification methods relate to the in vitro production of definitive endoderm cells from human embryonic stem cells.

Using the methods described herein, cell populations or cell cultures can be enriched in definitive endoderm cell content by at least about 2- to about 1000-fold as compared to untreated or unenriched cell populations or cell cultures. In some embodiments, definitive endoderm cells can be enriched by at least about 5- to about 500-fold as compared to untreated or unenriched cell populations or cell cultures. In other embodiments, definitive endoderm cells can be enriched from at least about 10- to about 200-fold as compared to untreated or unenriched cell populations or cell cultures. In still other embodiments, definitive endoderm cells can be enriched from at least about 20- to about 100-fold as compared to untreated or unenriched cell populations or cell cultures. In yet other embodiments, definitive endoderm cells can be enriched from at least about 40- to about 80-fold as compared to untreated or unenriched cell populations or cell cultures. In certain embodiments, definitive endoderm cells can be enriched from at least about 2- to about 20-fold as compared to untreated or unenriched cell populations or cell cultures.

In preferred embodiments, definitive endoderm cells are enriched, isolated and/or purified from other non-definitive endoderm cells after the stem cell cultures are induced to differentiate towards the definitive endoderm lineage. It will be appreciated that the above-described enrichment, isolation and purification procedures can be used with such cultures at any stage of differentiation.

In addition to the procedures just described, definitive endoderm cells may also be isolated by other techniques for cell isolation. Additionally, definitive endoderm cells may also be enriched or isolated by methods of serial subculture in growth conditions which promote the selective survival or selective expansion of said definitive endoderm cells.

Compositions Comprising Definitive Endoderm

Cell compositions produced by the above-described methods include cell cultures comprising definitive endoderm and cell populations enriched in definitive endoderm. For example, cell cultures which comprise definitive endoderm cells, wherein at least about 50-80% of the cells in culture are definitive endoderm cells, can be produced. Because the efficiency of the differentiation process can be adjusted by modifying certain parameters, which include but are not limited to, cell growth conditions, growth factor concentrations and the timing of culture steps, the differentiation procedures described herein can result in about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or greater than about 95% conversion of pluripotent cells to definitive endoderm. In processes in which isolation of definitive endoderm cells is employed, for example, by using an affinity reagent that binds to a marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1, a substantially pure definitive endoderm cell population can be recovered.

Some embodiments described herein relate to compositions, such as cell populations and cell cultures, that comprise both pluripotent cells, such as stem cells, and definitive endoderm cells. For example, using the methods described herein, compositions comprising mixtures of hESCs and definitive endoderm cells can be produced. In some embodiments, compositions comprising at least about 5 definitive endoderm cells for about every 95 pluripotent cells are produced. In other embodiments, compositions comprising at least about 95 definitive endoderm cells for about every 5 pluripotent cells are produced. Additionally, compositions comprising other ratios of definitive endoderm cells to pluripotent cells are contemplated. For example, compositions comprising at least about 1 definitive endoderm cell for about every 1,000,000 pluripotent cells, at least about 1 definitive endoderm cell for about every 100,000 pluripotent cells, at least about 1 definitive endoderm cell for about every 10,000 pluripotent cells, at least about 1 definitive endoderm cell for about every 1000 pluripotent cells, at least about 1 definitive endoderm cell for about every 500 pluripotent cells, at least about 1 definitive endoderm cell for about every 100 pluripotent cells, at least about 1 definitive endoderm cell for about every 10 pluripotent cells, at least about 1 definitive endoderm cell for about every 5 pluripotent cells, at least about 1 definitive endoderm cell for about every 2 pluripotent cells, at least about 2 definitive endoderm cells for about every 1 pluripotent cell, at least about 5 definitive endoderm cells for about every 1 pluripotent cell, at least about 10 definitive endoderm cells for about every 1 pluripotent cell, at least about 20 definitive endoderm cells for about every 1 pluripotent cell, at least about 50 definitive endoderm cells for about every 1 pluripotent cell, at least about 100 definitive endoderm cells for about every 1 pluripotent cell, at least about 1000 definitive endoderm cells for about every 1 pluripotent cell, at least about 10,000 definitive endoderm cells for about every 1 pluripotent cell, at least about 100,000 definitive endoderm cells for about every 1 pluripotent cell and at least about 1,000,000 definitive endoderm cells for about every 1 pluripotent cell are contemplated. In some embodiments, the pluripotent cells are human pluripotent stem cells. In certain embodiments the stem cells are derived from a morula, the inner cell mass of an embryo or the gonadal ridges of an embryo. In certain other embodiments, the pluripotent cells are derived from the gondal or germ tissues of a multicellular structure that has developed past the embryonic stage.

Some embodiments described herein relate to cell cultures or cell populations comprising from at least about 5% definitive endoderm cells to at least about 95% definitive endoderm cells. In some embodiments the cell cultures or cell populations comprise mammalian cells. In preferred embodiments, the cell cultures or cell populations comprise human cells. For example, certain specific embodiments relate to cell cultures comprising human cells, wherein from at least about 5% to at least about 95% of the human cells are definitive endoderm cells. Other embodiments relate to cell cultures comprising human cells, wherein at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90% or greater than 90% of the human cells are definitive endoderm cells. In embodiments where the cell cultures or cell populations comprise human feeder cells, the above percentages are calculated without respect to the human feeder cells in the cell cultures or cell populations.

Further embodiments described herein relate to compositions, such as cell cultures or cell populations, comprising human cells, such as human definitive endoderm cells, wherein the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is greater than the expression of the OCT4, SPARC, alpha-fetoprotein (AFP), Thrombomodulin (TM) and/or SOX7 marker in at least about 5% of the human cells. In other embodiments, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in greater than 95% of the human cells. In embodiments where the cell cultures or cell populations comprise human feeder cells, the above percentages are calculated without respect to the human feeder cells in the cell cultures or cell populations. In certain embodiments, the definitive endoderm cells expressing SOX17, CXCR4 and/or one or more other markers selected from Table 3 do not express significant levels or amounts of PDX1 (PDX1-negative).

It will be appreciated that some embodiments described herein relate to compositions, such as cell cultures or cell populations, comprising human cells, such as human definitive endoderm cells, wherein the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 markers in from at least about 5% to greater than at least about 95% of the human cells. In other embodiments, the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in greater than 95% of the human cells. In embodiments where the cell cultures or cell populations comprise human feeder cells, the above percentages are calculated without respect to the human feeder cells in the cell cultures or cell populations. In certain embodiments, the definitive endoderm cells expressing one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 do not express significant levels or amounts of PDX1 (PDX1-negative).

Additional embodiments described herein relate to compositions, such as cell cultures or cell populations, comprising mammalian endodermal cells, such as human endoderm cells, wherein the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at least about 5% of the endodermal cells. In other embodiments, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at least about 10% of the endodermal cells, in at least about 15% of the endodermal cells, in at least about 20% of the endodermal cells, in at least about 25% of the endodermal cells, in at least about 30% of the endodermal cells, in at least about 35% of the endodermal cells, in at least about 40% of the endodermal cells, in at least about 45% of the endodermal cells, in at least about 50% of the endodermal cells, in at least about 55% of the endodermal cells, in at least about 60% of the endodermal cells, in at least about 65% of the endodermal cells, in at least about 70% of the endodermal cells, in at least about 75% of the endodermal cells, in at least about 80% of the endodermal cells, in at least about 85% of the endodermal cells, in at least about 90% of the endodermal cells, in at least about 95% of the endodermal cells or in greater than 95% of the endodermal cells. In certain embodiments, the mammalian endodermal cells expressing SOX17, CXCR4 and/or one or more other markers selected from Table 3 do not express significant levels or amounts of PDX1 (PDX1-negative).

It will be appreciated that some embodiments described herein relate to compositions, such as cell cultures or cell populations comprising mammalian endodermal cells, wherein the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 markers in from at least about 5% to greater than at least about 95% of the endodermal cells. In other embodiments, the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at least about 10% of the endodermal cells, in at least about 15% of the endodermal cells, in at least about 20% of the endodermal cells, in at least about 25% of the endodermal cells, in at least about 30% of the endodermal cells, in at least about 35% of the endodermal cells, in at least about 40% of the endodermal cells, in at least about 45% of the endodermal cells, in at least about 50% of the endodermal cells, in at least about 55% of the endodermal cells, in at least about 60% of the endodermal cells, in at least about 65% of the endodermal cells, in at least about 70% of the endodermal cells, in at least about 75% of the endodermal cells, in at least about 80% of the endodermal cells, in at least about 85% of the endodermal cells, in at least about 90% of the endodermal cells, in at least about 95% of the endodermal cells or in greater than 95% of the endodermal cells. In certain embodiments, the mammalian endodermal cells expressing one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 do not express significant levels or amounts of PDX1 (PDX1-negative).

Further embodiments described herein relate to compositions, such as cell cultures or cell populations, comprising human cells, such as human definitive endoderm cells, wherein the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is greater than the expression of the OCT4, SPARC, alpha-fetoprotein (AFP), Thrombomodulin (TM) and/or SOX7 marker in at least about 5% of the human cells. In other embodiments, the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in greater than 95% of the human cells. In embodiments where the cell cultures or cell populations comprise human feeder cells, the above percentages are calculated without respect to the human feeder cells in the cell cultures or cell populations. In certain embodiments, the definitive endoderm cells expressing SOX17, CXCR4 and/or one or more other markers selected from Table 3 do not express significant levels or amounts of PDX1 (PDX1-negative).

It will be appreciated that some embodiments described herein relate to compositions, such as cell cultures or cell populations, comprising human cells, such as human definitive endoderm cells, wherein the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 markers in from at least about 5% to greater than at least about 95% of the human cells. In other embodiments, the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in greater than 95% of the human cells. In embodiments where the cell cultures or cell populations comprise human feeder cells, the above percentages are calculated without respect to the human feeder cells in the cell cultures or cell populations. In certain embodiments, the definitive endoderm cells expressing one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 do not express significant levels or amounts of PDX1 (PDX1-negative).

Using the methods described herein, compositions comprising definitive endoderm cells substantially free of other cell types can be produced. In some embodiments described herein, the definitive endoderm cell populations or cell cultures produced by the methods described herein are substantially free of cells that significantly express the OCT4, SOX7, AFP, SPARC, TM, ZIC1 or BRACH marker genes.

Some embodiments described herein relate to enriched, isolated and/or purified compositions, such as cell cultures or cell populations, comprising human cells, such as human definitive endoderm cells, wherein the expression of SOX17, CXCR4 and/or one or more other markers selected from Table 3 is greater than the expression of the OCT4, SPARC, alpha-fetoprotein (AFP), Thrombomodulin (TM) and/or SOX7 marker in at least about 96% of the human cells, in at least about 97% of the human cells, in at least about 98% of the human cells, in at least about 99% of the human cells or in at least about 100% of the human cells. In certain embodiments, enriched, isolated and/or purified compositions of definitive endoderm cells expressing SOX17, CXCR4 and/or one or more other markers selected from Table 3 do not express significant levels or amounts of PDX1 (PDX1-negative).

It will be appreciated that some embodiments described herein relate to enriched, isolated and/or purified compositions, such as cell cultures or cell populations, comprising human cells, such as human definitive endoderm cells, wherein the expression of one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is greater than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 markers in from at least about 96%, in at least about 97% of the human cells, in at least about 98% of the human cells, in at least about 99% of the human cells or in at least about 100% of the human cells. In certain embodiments, the enriched, isolated and/or purified definitive endoderm cells expressing one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 do not express significant levels or amounts of PDX1 (PDX1-negative).

In one embodiment, a description of a definitive endoderm cell based on the expression of marker genes is, SOX17 high, MIXL1 high, AFP low, SPARC low, Thrombomodulin low, SOX7 low, CXCR4 high. In other embodiments, a description of a definitive endoderm cell based on the expression of marker genes is one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 high; AFP low; SPARC low; Thrombomodulin low and SOX7 low.

Reagent-Cell Complexes

Some aspects of the present invention relate to compositions, such as cell cultures and/or cell population, that comprise complexes of one or more definitive endoderm cells bound to one or more reagents (reagent-cell complexes). For example, cell cultures and/or cell populations comprising reagent-cell complexes, wherein at least about 5 to at least about 100% of the definitive endoderm cells in culture are in the form of reagent-cell complexes, can be produced. In other embodiments, cell cultures and/or cell populations can be produced which comprise at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or at least about 100% reagent-cell complexes. In some embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more antibodies that bind to a marker selected from Table 3. In preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more antibodies that bind to a marker selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more antibodies that bind to a marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. In still other embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more ligands that bind to a marker selected Table 3. In preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more ligands that bind to a marker selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more ligands that bind to a marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

Some embodiments described herein relate to cell cultures and/or cell populations comprising from at least about 5% reagent cell complexes to at least about 95% reagent-cell complexes. In some embodiments the cell cultures or cell populations comprise mammalian cells. In preferred embodiments, the cell cultures or cell populations comprise human cells. For example, certain specific embodiments relate to cell cultures comprising human cells, wherein from at least about 5% to at least about 95% of the human cells are definitive endoderm cells. Other embodiments relate to cell cultures comprising human cells, wherein at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90% or greater than 90% of the human cells are reagent cell complexes. In embodiments where the cell cultures or cell populations comprise human feeder cells, the above percentages are calculated without respect to the human feeder cells in the cell cultures or cell populations. In some embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more antibodies that bind to a marker selected from Table 3. In preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more antibodies that bind to a marker selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more antibodies that bind to a marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. In still other embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more ligands that bind to a marker selected Table 3. In preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more ligands that bind to a marker selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other preferred embodiments, the reagent cell complexes comprise one or more definitive endoderm cells bound to one or more ligands that bind to a marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

In some embodiments, the definitive endoderm cells present in the reagent-cell complexes that have been described above express SOX17, CXCR4 and/or one or more other markers selected from Table 3 to a greater extent than OCT4, SPARC, alpha-fetoprotein (AFP), Thrombomodulin (TM) and/or SOX7. In preferred embodiments, the definitive endoderm cells expressing SOX17, CXCR4 and/or one or more other markers selected from Table 3 do not express significant levels or amounts of PDX1 (PDX1-negative). In other embodiments, the definitive endoderm cells present in the reagent-cell complexes that have been described above express one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 to a greater extent than OCT4, SPARC, AFP, TM and/or SOX7. In preferred embodiments, the definitive endoderm cells expressing one or more markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 do not express significant levels or amounts of PDX1 (PDX1-negative). In yet other embodiments, the definitive endoderm cells present in the reagent-cell complexes that have been described above express one or more cell-surface markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1. In preferred embodiments, the definitive endoderm cells expressing one or more cell-surface markers selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

Additional embodiments described herein relate to compositions, such as cell cultures and/or cell populations, that comprise both pluripotent cells, such as stem cells, and reagent-cell complexes. For example, using the methods described herein, compositions comprising mixtures of hESCs and reagent-cell complexes of definitive endoderm cells can be produced. In some embodiments, compositions comprising at least about 5 reagent-cell complexes for about every 95 pluripotent cells are provided. In other embodiments, compositions comprising at least about 95 reagent-cell complexes for about every 5 pluripotent cells are provided. Additionally, compositions comprising other ratios of reagent-cell complexes cells to pluripotent cells are contemplated. For example, compositions comprising at least about 1 reagent-cell complex for about every 1,000,000 pluripotent cells, at least about 1 reagent-cell complex for about every 100,000 pluripotent cells, at least about 1 reagent-cell complex cell for about every 10,000 pluripotent cells, at least about 1 reagent-cell complex for about every 1000 pluripotent cells, at least about 1 reagent-cell complex for about every 500 pluripotent cells, at least about 1 reagent-cell complex for about every 100 pluripotent cells, at least about 1 reagent-cell complex for about every 10 pluripotent cells, at least about 1 reagent-cell complex for about every 5 pluripotent cells, at least about 1 reagent-cell complex for about every 2 pluripotent cells, at least about reagent-cell complexes for about every 1 pluripotent cell, at least about 5 reagent-cell complexes for about every 1 pluripotent cell, at least about 10 definitive endoderm cells for about every 1 pluripotent cell, at least about 20 reagent-cell complexes for about every 1 pluripotent cell, at least about 50 reagent-cell complexes for about every 1 pluripotent cell, at least about reagent-cell complexes for about every 1 pluripotent cell, at least about 1000 reagent-cell complexes for about every 1 pluripotent cell, at least about 10,000 reagent-cell complexes for about every 1 pluripotent cell, at least about 100,000 reagent-cell complexes for about every 1 pluripotent cell and at least about 1,000,000 reagent-cell complexes for about every 1 pluripotent cell are contemplated. In some embodiments of the present invention, the pluripotent cells are human pluripotent stem cells. In certain embodiments the stem cells are derived from a morula, the inner cell mass of an embryo or the gonadal ridges of an embryo. In certain other embodiments, the pluripotent cells are derived from the gondal or germ tissues of a multicellular structure that has developed past the embryonic stage.

Identification and Quantitation of Definitive Endoderm Cells

The desirability of detecting or determining the amount of definitive endoderm cells in a cell culture or cell population, and methods of distinguishing this cell type from the other cells in the culture or in the population is readily apparent. Accordingly, certain embodiments described herein relate to reagents and methods for the detection, identification, and quantitation of cell markers whose presence, absence and/or relative expression levels are indicative for definitive endoderm.

Some embodiments provide a method of detecting definitive endoderm cells in a cell population that includes the steps of detecting the expression of at least one of the markers described in Table 3. In some embodiments, the method also includes the step of detecting the expression of at least one marker selected from the group consisting of OCT4, AFP, TM, SPARC and SOX7. In certain embodiments, the expression of one or more markers selected from Table 3 is greater than the expression of OCT4, AFP, TM, SPARC, or SOX7.

As discussed below, expression levels of the markers may be determined by any method known to those skilled in the art, including but not limited to immunocytochemistry or quantitative PCR (Q-PCR). Embodiments of the present invention relate to compositions useful in the detection and quantitation of definitive endoderm cells.

Immunodetection of Definitive Endoderm

In some embodiments, immunochemistry is used to detect the presence, absence, and/or level of expression of proteins encoded by the above-mentioned genes. Accordingly, some embodiments relate to isolated antibodies that bind to certain markers, such as any of the polypeptides encoded by the nucleic acids described in Table 3 including, but not limited to, AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. Preferred embodiments relate to antibodies that bind to CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

The term “antibody” is used in the broadest sense and unless specified specifically covers single monoclonal antibodies (including agonist and antagonist antibodies) and antibody compositions with polyepitopic specificity. The term “antibody” also includes obvious variants, derivatives, analogs, fragments, mimetics, all of which substantially retain the binding characteristics and other properties of the stated antibody.

Monoclonal antibodies (moAbs) refer to antibodies obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. In some embodiments, monoclonal antibodies may be highly specific, being directed against a single epitopic region of an antigen. Furthermore, in contrast to conventional (polyclonal) antibody preparations that typically include different antibodies directed against different determinants (epitopes), each moAb is directed against a single determinant on the antigen. In addition to their specificity, monoclonal antibodies are advantageous in that they can be synthesized by hybridoma culture, uncontaminated by other immunoglobulins.

The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. As described above, the monoclonal antibodies to be used in accordance with the invention may be made by the hybridoma method first described by Kohler et al., Nature, 256:495 (1975), or may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567 to Cabilly et al.). The “monoclonal antibodies” also include clones of antigen-recognition and binding-site containing antibody fragments (Fv clones) isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991), for example.

Furthermore, as described above, in some embodiments, the antibodies can be “antibody fragments,” which refer to a portion of an intact antibody comprising the antigen binding site or variable region of the intact antibody, wherein the portion is free of the constant heavy chain domains of the Fc region of the intact antibody. Examples of antibody fragments include Fab, Fab′, Fab′-SH, F(ab′)₂, and Fv fragments; diabodies; any antibody fragment that is a polypeptide having a primary structure consisting of one uninterrupted sequence of contiguous amino acid residues (referred to herein as a “single-chain antibody fragment” or “single chain polypeptide”), including without limitation (1) single-chain Fv (scFv) molecules; (2) single chain polypeptides containing only one light chain variable domain, or a fragment thereof that contains the three CDRs of the light chain variable domain, without an associated heavy chain moiety; and (3) single chain polypeptides containing only one heavy chain variable region, or a fragment thereof containing the three CDRs of the heavy chain variable region, without an associated light chain moiety. In some embodiments, antibody fragments further encompass multispecific or multivalent structures formed from the aforementioned antibody fragments.

It will be appreciated that a wide variety of techniques are useful for the immunodetection of molecules including the markers described herein. For example, flow cytometry, immunomicroscopy, Western blotting, direct and indirect sandwich assays, such as ELISA, Western blotting, and the like. These techniques are described, herein and, for example in Malik and Lillehoj (19994), herein incorporated by reference in its entirety.

Nucleic Acid-Based Detection of Definitive Endoderm

In other embodiments, nucleic acid hybridization and/or amplification techniques are used to detect the presence, absence and/or level of expression of a marker. For example, the amount of transcript produced by certain genetic markers, such as any of the markers listed in Table 3, including but not limited to AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192, can be determined by nucleic acid hybridization techniques, such as, for example, Northern blots, slot blots, RNase protection, in, situ hybridization, and the like. Techniques for the detection and quantitation of specific nucleic acids are well-known to those skilled in the art and are described in, for example, Ausubel et al., (1997), Current Protocols of Molecular Biology, John Wiley and Sons (1997); Gene transcription: RNA analysis: essential techniques. 1996. K. Docherty (ed.), Chichester; and Reue, K, mRNA Quantitation Techniques: Considerations for Experimental Design and Application, (1998), J. Nutr., 128(11):2038-2044, each of which is herein incorporated by reference in their entirety. Several sophisticated techniques exist for the sensitive and specific detection nucleic acids

In some embodiments, nucleic acid detection techniques such as those described herein are used in combination with nucleic acid amplification techniques. Several nucleic acid amplification techniques are also useful in detection of the presence/absence and/or level of expression markers. The skilled artisan will appreciate that any nucleic acid amplification method that can be adapted to detect expression levels of genes, such as ligase chain reaction (LCR) (See, Wu (1989) Genomics 4:560; Landegren (1988) Science 241:1077; Barringer (1990) Gene 89:117), nucleic acid sequence-based amplification (NASBA), self-sustained sequence replication (3SR) (See, Guatelli (1990) Proc. Natl. Acad. Sci. USA, 87:1874), strand displacement amplification (SDA), transcription-mediated amplification (TMA) (See, Kwoh (1989) Proc. Natl. Acad Sci. USA 86:1173), cycling probe technology (CPT), solid phase amplification (SPA), nuclease dependent signal amplification (NDSA), rolling circle amplification technology (RCA), Anchored strand displacement amplification, solid-phase (immobilized) rolling circle amplification, Q Beta replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA, Cangene, Mississauga, Ontario) are useful in the methods described herein. These and other techniques are also described in Berger (1987) Methods Enzymol. 152:307-316; Sambrook, Ausubel, Mullis (1987) U.S. Pat. Nos. 4,683,195 and 4,683,202; Amheim (1990) C&EN 36-47; Lomell J. Clin. Chem., 35:1826 (1989); Van Brunt, Biotechnology, 8:291-294 (1990); Wu (1989) Gene 4:560; Sooknanan (1995) Biotechnology 13:563-564. For example, several real-time reverse-transcription-PCR (RT-PCR) based techniques are available that enable mRNA detection and quantitation.

Detection and quantitation of nucleic acids is also known to those skilled in the art. Non-limiting examples of amplification and detection techniques include, for example, TaqMan probe technology (See, European Patent EP 0 543 942), molecular beacon probe technology (See, Tyagi et al., (1996) Nat. Biotech. 14:303-308.), Scorpion probe technology (See, Thewell (2000), Nucl. Acids Res. 28:3752), nanoparticle probe technology (See, Elghanian, et al. (1997) Science 277:1078-1081.) and Amplifluor probe technology (See, U.S. Pat. Nos. 5,866,366; 6,090,592; 6,117,635; and 6,117,986), fluorescence resonance energy transfer (FRET)-based methods such as adjacent hybridization of probes (including probe-probe and probe-primer methods) (See, J. R. Lakowicz, “Principles of Fluorescence Spectroscopy,” Kluwer Academic/Plenum Publishers, New York, 1999).

Accordingly, some embodiments of the present invention relate to compositions useful in nucleic acid based techniques for the detection, identification and/or quantitation of definitive endoderm cells in a cell population. Some embodiments relate to composition that include a first oligonucleotide that hybridizes to a first marker, such as those described herein, and a second oligonucleotide that hybridizes to a second marker that other than the first marker, such as those described herein. By way of example, the first and second oligonucleotides can hybridize to different markers selected from Table 3. In preferred embodiments, the first and second oligonucleotides can hybridize to different markers selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In other preferred embodiments, the oligonucleotides hybridize to the above markers under stringent conditions.

As used herein, oligonucleotides refer to polynucleotides that are generally at least about 10 nucleotides in length, at least about 12 nucleotides in length, at least about 14 nucleotides in length, at least about 16 nucleotides in length, at least about 18 nucleotides in length, at least about 20 nucleotides in length, at least about 22 nucleotides in length, at least about 24 nucleotides in length, at least about 26 nucleotides in length, at least about 28 nucleotides in length, at least about 30 nucleotides in length, at least about 35 nucleotides in length, at least about 40 nucleotides in length, at least about 45 nucleotides in length, at least about 50 nucleotides in length or greater than 50 nucleotides in length.

It will be appreciated by one skilled in the art that hybridization of the oligonucleotides to marker sequence is achieved by selecting sequences which are at least substantially complementary to the target or reference nucleic acid sequence. In some embodiments, this includes base-pairing of the oligonucleotide target nucleic acid sequence over the entire length of the oligonucleotide sequence. Such sequences can be referred to as “fully complementary” with respect to each other. Where an oligonucleotide is referred to as “substantially complementary” with respect to a nucleic acid sequence herein, the two sequences can be fully complementary, or they may form mismatches upon hybridization, but retain the ability to hybridize under the conditions used to detect the presence marker.

As set forth above, oligonucleotides of the embodiments described herein may be used in an amplification reaction. Accordingly, the compositions may include a polymerase, such as an RNA-dependent DNA polymerase. In some embodiments, the RNA-dependent DNA polymerase is a reverse transciptase. Moloney Murine Leukemia Virus reverse transcriptase and Avian Myeloblastosis Virus (AMV) reverse transcriptase are non-limiting examples of reverse transcriptase enzymes commonly used by those skilled in the art and which are useful in the embodiments described herein. Further embodiments may also include DNA-dependent DNA polymerases, such as Taq polymerase and the like.

Advantageously, the oligonucleotides described herein can include a label, such as a radioactive label, a fluorescent label, or any other type of label that facilitates the detection and/or quantitation of nucleic acid markers, such as those described herein.

In still other embodiments, Q-PCR and immunohistochemical techniques are both used to identify and determine the amount or relative proportions of such markers.

Identification of Factors Capable of Promoting the Differentiation of Definitive Endoderm Cells

Certain screening methods described herein relate to methods for identifying at least one differentiation factor that is capable of promoting the differentiation of definitive endoderm cells. In some embodiments of these methods, cell populations comprising definitive endoderm cells, such as human definitive endoderm cells, are obtained. The cell population is then provided with a candidate differentiation factor. At a first time point, which is prior to or at approximately the same time as providing the candidate differentiation factor, expression of a marker is determined. Alternatively, expression of the marker can be determined after providing the candidate differentiation factor. At a second time point, which is subsequent to the first time point and subsequent to the step of providing the candidate differentiation factor to the cell population, expression of the same marker is again determined. Whether the candidate differentiation factor is capable of promoting the differentiation of the definitive endoderm cells is determined by comparing expression of the marker at the first time point with the expression of the marker at the second time point. If expression of the marker at the second time point is increased or decreased as compared to expression of the marker at the first time point, then the candidate differentiation factor is capable of promoting the differentiation of definitive endoderm cells.

Some embodiments of the screening methods described herein utilize cell populations or cell cultures which comprise human definitive endoderm cells. For example, the cell population can be a substantially purified population of human definitive endoderm cells. Alternatively, the cell population can be an enriched population of human definitive endoderm cells, wherein at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97% or greater than at least about 97% of the human cells in the cell population are human definitive endoderm cells. In other embodiments described herein, the cell population comprises human cells wherein at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85% or greater than at least about 85% of the human cells are human definitive endoderm cells. In some embodiments, the cell population includes non-human cells such as non-human feeder cells. In other embodiments, the cell population includes human feeder cells. In such embodiments, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% or greater than at least about 95% of the human cells, other than said feeder cells, are human definitive endoderm cells.

In embodiments of the screening methods described herein, the cell population is contacted or otherwise provided with a candidate (test) differentiation factor. The candidate differentiation factor can comprise any molecule that may have the potential to promote the differentiation of human definitive endoderm cells. In some embodiments described herein, the candidate differentiation factor comprises a molecule that is known to be a differentiation factor for one or more types of cells. In alternate embodiments, the candidate differentiation factor comprises a molecule that in not known to promote cell differentiation. In preferred embodiments, the candidate differentiation factor comprises molecule that is not known to promote the differentiation of human definitive endoderm cells.

In some embodiments of the screening methods described herein, the candidate differentiation factor comprises a small molecule. In preferred embodiments, a small molecule is a molecule having a molecular mass of about 10,000 amu or less. In some embodiments, the small molecule comprises a retinoid. In some embodiments, the small molecule comprises retinoic acid.

In other embodiments described herein, the candidate differentiation factor comprises a polypeptide. The polypeptide can be any polypeptide including, but not limited to, a glycoprotein, a lipoprotein, an extracellular matrix protein, a cytokine, a chemokine, a peptide hormone, an interleukin or a growth factor. Preferred polypeptides include growth factors. In some preferred embodiments, the candidate differentiation factors comprises one or more growth factors selected from the group consisting of FGF10, FGF4, FGF2, Wnt3A and Wnt3B.

In some embodiments of the screening methods described herein, the candidate differentiation factors comprise one or more growth factors selected from the group consisting of Amphiregulin, B-lymphocyte stimulator, IL-16, Thymopoietin, TRAIL/Apo-2, Pre B cell colony enhancing factor, Endothelial differentiation-related factor 1 (EDF1), Endothelial monocyte activating polypeptide II, Macrophage migration inhibitory factor (MIF), Natural killer cell enhancing factor (NKEFA), Bone mophogenetic protein 2, Bone mophogenetic protein 8 (osteogeneic protein 2), Bone morphogenic protein 6, Bone morphogenic protein 7, Connective tissue growth factor (CTGF), CGI-149 protein (neuroendocrine differentiation factor), Cytokine A3 (macrophage inflammatory protein 1-alpha), Gliablastoma cell differentiation-related protein (GBDR1), Hepatoma-derived growth factor, Neuromedin U-25 precursor, Vascular endothelial growth factor (VEGF), Vascular endothelial growth factor B (VEGF-B), T-cell specific RANTES precursor, thymic dendritic cell-derived factor 1, Transferrin, Interleukin-1 (IL 1), Interleukin-2 (IL 2), Interleukin-3 (IL 3), Interleukin-4 (IL 4), Interleukin-5 (IL 5), Interleukin-6 (IL 6), Interleukin-7 (IL 7), Interleukin-8 (IL 8), Interleukin-9 (IL 9), Interleukin-10 (IL 10), Interleukin-11 (IL 11), Interleukin-12 (IL 12), Interleukin-13 (IL 13), Granulocyte-colony stimulating factor (G-CSF), Granulocyte macrophage colony stimulating factor (GM-CSF), Macrophage colony stimulating factor (M-CSF), Erythropoietin, Thrombopoietin, Vitamin D₃, Epidermal growth factor (EGF), Brain-derived neurotrophic factor, Leukemia inhibitory factor, Thyroid hormone, Basic fibroblast growth factor (bFGF), aFGF, FGF-4, FGF-6, Keratinocyte growth factor (KGF), Platelet-derived growth factor (PDGF), Platelet-derived growth factor-BB, beta nerve growth factor, activin A, Transforming growth factor beta 1 (TGF-β1), Interferon-α, Interferon-β, Interferon-γ, Tumor necrosis factor-α, Tumor necrosis factor-β, Burst promoting activity (BPA), Erythroid promoting activity (EPA), PGE₂, insulin growth factor-1 (IGF-1), IGF-II, Neutrophin growth factor (NGF), Neutrophin-3, Neutrophin 4/5, Ciliary neurotrophic factor, Glial-derived nexin, Dexamethasone, β-mercaptoethanol, Retinoic acid, Butylated hydroxyanisole, 5-azacytidine, Amphotericin B, Ascorbic acid, Ascrorbate, isobutylxanthine, indomethacin, β-glycerolphosphate, nicotinamide, DMSO, Thiazolidinediones, TWS119, oxytocin, vasopressin, melanocyte-stimulating hormone, corticortropin, lipotropin, thyrotropin, growth hormone, prolactin, luteinizing hormone, human chorionic gonadotropin, follicle stimulating hormone, corticotropin-releasing factor, gonadotropin-releasing factor, prolactin-releasing factor, prolactin-inhibiting factor, growth-hormone releasing factor, somatostatin, thyrotropin-releasing factor, calcitonin gene-related peptide, parathyroid hormone, glucagon-like peptide 1, glucose-dependent insulinotropic polypeptide, gastrin, secretin, cholecystokinin, motilin, vasoactive intestinal peptide, substance P, pancreatic polypeptide, peptide tyrosine tyrosine, neuropeptide tyrosine, insulin, glucagon, placental lactogen, relaxin, angiotensin II, calctriol, atrial natriuretic peptide, and melatonin, thyroxine, triiodothyronine, calcitonin, estradiol, estrone, progesterone, testosterone, cortisol, corticosterone, aldosterone, epinephrine, norepinepherine, androstiene, calcitriol, collagen, Dexamethasone, β-mercaptoethanol, Retinoic acid, Butylated hydroxyanisole, 5-azacytidine, Amphotericin B, Ascorbic acid, Ascrorbate, isobutylxanthine, indomethacin, β-glycerolphosphate, nicotinamide, DMSO, Thiazolidinediones, and TWS119.

In some embodiments of the screening methods described herein, the candidate differentiation factor is provided to the cell population in one or more concentrations. In some embodiments, the candidate differentiation factor is provided to the cell population so that the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 0.1 ng/ml to about 10 mg/ml. In some embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 1 ng/ml to about 1 mg/ml. In other embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 10 ng/ml to about 100 ng/ml. In still other embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 100 ng/ml to about 10 ng/ml. In preferred embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells is about 5 ng/ml, about 25 ng/ml, about 50 ng/ml, about 75 ng/ml, about 100 ng/ml, about 125 ng/ml, about 150 ng/ml, about 175 ng/ml, about 200 ng/ml, about 225 ng/ml, about 250 ng/ml, about 275 ng/ml, about 300 ng/ml, about 325 ng/ml, about 350 ng/ml, about 375 ng/ml, about 400 ng/ml, about 425 ng/ml, about 450 ng/ml, about 475 ng/ml, about 500 ng/ml, about 525 ng/ml, about 550 ng/ml, about 575 ng/ml, about 600 ng/ml, about 625 ng/ml, about 650 ng/ml, about 675 ng/ml, about 700 ng/ml, about 725 ng/ml, about 750 ng/ml, about 775 ng/ml, about 800 ng/ml, about 825 ng/ml, about 850 ng/ml, about 875 ng/ml, about 900 ng/ml, about 925 ng/ml, about 950 ng/ml, about 975 ng/ml, about 1 μg/ml, about 2 μg/ml, about 3 μg/ml, about 4 μg/ml, about 5 μg/ml, about 6 μg/ml, about 7 μg/ml, about 8 μg/ml, about 9 μg/ml, about 10 μg/ml, about 11 μg/ml, about 12 μg/ml, about 13 μg/ml, about 14 μg/ml, about 15 μg/ml, about 16 μg/ml, about 17 μg/ml, about 18 μg/ml, about 19 μg/ml, about 20 μg/ml, about 25 μg/ml, about 50 μg/ml, about 75 μg/ml, about 100 μg/ml, about 125 μg/ml, about 150 μg/ml, about 175 μg/ml, about 200 μg/ml, about 250 μg/ml, about 300 μg/ml, about 350 μg/ml, about 400 μg/ml, about 450 μg/ml, about 500 μg/ml, about 550 μg/ml, about 600 μg/ml, about 650 μg/ml, about 700 μg/ml, about 750 μg/ml, about 800 μg/ml, about 850 μg/ml, about 900 μg/ml, about 950 μg/ml, about 1000 μg/ml or greater than about 1000 μg/ml.

In certain embodiments of the screening methods described herein, the cell population is provided with a candidate differentiation factor which comprises any molecule other than foregut differentiation factor. For example, in some embodiments, the cell population is provided with a candidate differentiation factor which comprises any molecule other than a retinoid, a member of the TGFβ superfamily of growth factors, FGF10 or FGF4. In some embodiments, the cell population is provided with a candidate differentiation factor which comprises any molecule other than retinoic acid.

In some embodiments, steps of the screening methods described herein comprise determining expression of at least one marker at a first time point and a second time point. In some of these embodiments, the first time point can be prior to or at approximately the same time as providing the cell population with the candidate differentiation factor. Alternatively, in some embodiments, the first time point is subsequent to providing the cell population with the candidate differentiation factor. In some embodiments, expression of a plurality of markers is determined at a first time point.

Some preferred markers for use in the above embodiments include one or more markers selected from Table 3. In other preferred embodiments, the one or more markers are selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In still other preferred embodiments, the one or more markers are selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

In addition to determining expression of at least one marker at a first time point, some embodiments of the screening methods described herein contemplate determining expression of at least one marker at a second time point, which is subsequent to the first time point and which is subsequent to providing the cell population with the candidate differentiation factor. In such embodiments, expression of the same marker is determined at both the first and second time points. In some embodiments, expression of a plurality of markers is determined at both the first and second time points. In such embodiments, expression of the same plurality of markers is determined at both the first and second time points. In some embodiments, marker expression is determined at a plurality of time points, each of which is subsequent to the first time point, and each of which is subsequent to providing the cell population with the candidate differentiation factor. In certain embodiments, marker expression is determined by Q-PCR. In other embodiments, marker expression is determined by immunocytochemistry.

Some preferred markers for use in the above embodiments include one or more markers selected from Table 3. In other preferred embodiments, the one or more markers are selected from the group consisting of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192. In still other preferred embodiments, the one or more markers are selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

In certain embodiments of the screening methods described herein, the marker having its expression is determined at the first and second time points is a marker that is associated with the differentiation of human definitive endoderm cells to cells which are the precursors of cells which make up tissues and/or organs that are derived from the gut tube. In some embodiments, the tissues and/or organs that are derived from the gut tube comprise terminally differentiated cells. In some embodiments, the marker is indicative of pancreatic cells or pancreatic precursor cells. In preferred embodiments, the marker is pancreatic-duodenal homeobox factor-1 (PDX1). In other embodiments, the marker is homeobox A13 (HOXA13) or homeobox C6 (HOXC6). Additionally, in other embodiments, the marker is indicative of liver cells or liver precursor cells. In certain preferred embodiments, the marker is albumin, hepatocyte specific antigen (HSA) or prospero-related homeobox 1 (PROX1). In other embodiments, the marker is indicative of lung or lung precursor cells. In some preferred embodiments, the marker is thyroid transcription factor 1 (TITF1). In yet other embodiments, the marker is indicative of intestinal or intestinal precursor cells. In additional preferred embodiments, the marker is villin, glucose transporter-2 (GLUT2), apolipoprotein A1 (APOA1), vascular cell adhesion molecule-1 (VACM1), von Willebrand factor (VWF), CXC-type chemokine receptor 4 (CXCR4) or caudal type homeobox transcription factor 2 (CDX2). In still other embodiments, the marker is indicative of stomach or stomach precursor cells. In additional preferred embodiments, the marker is VCAM1, VWF or CXCR4. In other embodiments, the marker is indicative of thyroid or thyroid precursor cells. In such embodiments, the marker is TITF1. In still other embodiments, the marker is indicative of thymus or thymus precursor cells.

In some embodiments of the screening methods described herein, sufficient time is allowed to pass between providing the cell population with the candidate differentiation factor and determining marker expression at the second time point. Sufficient time between providing the cell population with the candidate differentiation factor and determining expression of the marker at the second time point can be as little as from about 1 hour to as much as about 10 days. In some embodiments, the expression of at least one marker is determined multiple times subsequent to providing the cell population with the candidate differentiation factor. In some embodiments, sufficient time is at least about 1 hour, at least about 6 hours, at least about 12 hours, at least about 18 hours, at least about 24 hours, at least about 30 hours, at least about 36 hours, at least about 42 hours, at least about 48 hours, at least about 54 hours, at least about 60 hours, at least about 66 hours, at least about 72 hours, at least about 78 hours, at least about 84 hours, at least about 90 hours, at least about 96 hours, at least about 102 hours, at least about 108 hours, at least about 114 hours, at least about 120 hours, at least about 126 hours, at least about 132 hours, at least about 138 hours, at least about 144 hours, at least about 150 hours, at least about 156 hours, at least about 162 hours, at least about 168 hours, at least about 174 hours, at least about 180 hours, at least about 186 hours, at least about 192 hours, at least about 198 hours, at least about 204 hours, at least about 210 hours, at least about 216 hours, at least about 222 hours, at least about 228 hours, at least about 234 hours or at least about 240 hours.

In some embodiments of the methods described herein, it is further determined whether the expression of the marker at the second time point has increased or decreased as compared to the expression of this marker at the first time point. An increase or decrease in the expression of the at least one marker indicates that the candidate differentiation factor is capable of promoting the differentiation of the definitive endoderm cells. Similarly, if expression of a plurality of markers is determined, it is further determined whether the expression of the plurality of markers at the second time point has increased or decreased as compared to the expression of this plurality of markers at the first time point. An increase or decrease in marker expression can be determined by measuring or otherwise evaluating the amount, level or activity of the marker in the cell population at the first and second time points. Such determination can be relative to other markers, for example housekeeping gene expression, or absolute. In certain embodiments, wherein marker expression is increased at the second time point as compared with the first time point, the amount of increase is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, at least about 100-fold or more than at least about 100-fold. In some embodiments, the amount of increase is less than 2-fold. In embodiments where marker expression is decreased at the second time point as compared with the first time point, the amount of decrease is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, at least about 100-fold or more than at least about 100-fold. In some embodiments, the amount of decrease is less than 2-fold.

In some embodiments of the screening methods described herein, after providing the cell population with a candidate differentiation factor, the human definitive endoderm cells differentiate into one or more cell types of the definitive endoderm lineage. In some embodiments, after providing the cell population with a candidate differentiation factor, the human definitive endoderm cells differentiate into cells that are derived from the gut tube. Such cells include, but are not limited to, cells of the pancreas, liver, lungs, stomach, intestine, thyroid, thymus, pharynx, gallbladder and urinary bladder as well as precursors of such cells. Additionally, these cells can further develop into higher order structures such as tissues and/or organs.

Having generally described this invention, a further understanding can be obtained by reference to certain specific examples which are provided herein for purposes of illustration only, and are not intended to be limiting.

Example 1 Human ES Cells

For our studies of endoderm development we employed human embryonic stem cells, which are pluripotent and can divide seemingly indefinitely in culture while maintaining a normal karyotype. ES cells were derived from the 5-day-old embryo inner cell mass using either immunological or mechanical methods for isolation. In particular, the human embryonic stem cell line hESCyt-25 was derived from a supernumerary frozen embryo from an in vitro fertilization cycle following informed consent by the patient. Upon thawing the hatched blastocyst was plated on mouse embryonic fibroblasts (MEF), in ES medium (DMEM, 20% FBS, non essential amino acids, beta-mercaptoethanol, and FGF2). The embryo adhered to the culture dish and after approximately two weeks, regions of undifferentiated hESCs were transferred to new dishes with MEFs. Transfer was accomplished with mechanical cutting and a brief digestion with dispase, followed by mechanical removal of the cell clusters, washing and re-plating. Since derivation, hESCyt-25 has been serially passaged over 100 times. We employed the hESCyt-25 human embryonic stem cell line as our starting material for the production of definitive endoderm.

It will be appreciated by those of skill in the art that stem cells or other pluripotent cells can also be used as starting material for the differentiation procedures described herein. For example, cells obtained from embryonic gonadal ridges, which can be isolated by methods known in the art, can be used as pluripotent cellular starting material.

Example 2 hESCyt-25 Characterization

The human embryonic stem cell line, hESCyt-25 has maintained a normal morphology, karyotype, growth and self-renewal properties over 18 months in culture. This cell line displays strong immunoreactivity for the OCT4, SSEA-4 and TRA-1-60 antigens, all of which, are characteristic of undifferentiated hESCs and displays alkaline phosphatase activity as well as a morphology identical to other established HESC lines. Furthermore, the human stem cell line, hESCyt-25, also readily forms embryoid bodies (EBs) when cultured in suspension. As a demonstration of its pluripotent nature, hESCyT-25 differentiates into various cell types that represent the three principal germ layers. Ectoderm production was demonstrated by Q-PCR for ZIC1 as well as immunocytochemistry (ICC) for nestin and more mature neuronal markers. Immunocytochemical staining for β-III tubulin was observed in clusters of elongated cells, characteristic of early neurons. Previously, we treated EBs in suspension with retinoic acid, to induce differentiation of pluripotent stem cells to visceral endoderm (VE), an extra-embryonic lineage. Treated cells expressed high levels of α-fetoprotein (AFP) and SOX7, two markers of VE, by 54 hours of treatment. Cells differentiated in monolayer expressed AFP in sporadic patches as demonstrated by immunocytochemical staining. As will be described below, the hESCyT-25 cell line was also capable of forming definitive endoderm, as validated by real-time quantitative polymerase chain reaction (Q-PCR) and immunocytochemistry for SOX17 and HNF3beta in the absence of AFP and SOX7 expression. To demonstrate differentiation to mesoderm, differentiating EBs were analyzed for Brachyury gene expression at several time points. Brachyury expression increased progressively over the course of the experiment. In view of the foregoing, the hESCyT-25 line is pluripotent as shown by the ability to form cells representing the three germ layers as well as extraembryonic lineages.

Example 3 Production of SOX17 Antibody

A primary obstacle to the identification of definitive endoderm in hESC cultures is the lack of appropriate tools. We therefore undertook the production of an antibody raised against human SOX17 protein.

The marker SOX17 is expressed throughout the definitive endoderm as it forms during gastrulation and its expression is maintained in the gut tube (although levels of expression vary along the A-P axis) until around the onset of organogenesis. SOX17 is also expressed in a subset of extra-embryonic endoderm cells. No expression of this protein has been observed in mesoderm or ectoderm. It has now been discovered that SOX17 is an appropriate marker for the definitive endoderm lineage when used in conjunction with markers to exclude extra-embryonic lineages.

As described in detail herein, the SOX17 antibody was utilized to specifically examine effects of various treatments and differentiation procedures aimed at the production of SOX17 positive definitive endoderm cells. Other antibodies reactive to AFP, SPARC and Thrombomodulin were also employed to rule out the production of visceral and parietal endoderm (extra-embryonic endoderm).

In order to produce an antibody against SOX17, a portion of the human SOX17 cDNA (SEQ ID NO: 1) corresponding to amino acids 172-414 (SEQ ID NO: 2) in the carboxyterminal end of the SOX17 protein (FIG. 2) was used for genetic immunization in rats at the antibody production company, GENOVAC (Freiberg, Germany), according to procedures developed there. Procedures for genetic immunization can be found in U.S. Pat. Nos. 5,830,876, 5,817,637, 6,165,993 and 6,261,281 as well as International Patent Application Publication Nos. WO00/29442 and WO99/13915, the disclosures of which are incorporated herein by reference in their entireties.

Other suitable methods for genetic immunization are also described in the non-patent literature. For example, Barry et al. describe the production of monoclonal antibodies by genetic immunization in Biotechniques 16: 616-620, 1994, the disclosure of which is incorporated herein by reference in its entirety. Specific examples of genetic immunization methods to produce antibodies against specific proteins can be found, for example, in Costaglia et al., (1998) Genetic immunization against the human thyrotropin receptor causes thyroiditis and allows production of monoclonal antibodies recognizing the native receptor, J. Immunol. 160: 1458-1465; Kilpatrick et al (1998) Gene gun delivered DNA-based immunizations mediate rapid production of murine monoclonal antibodies to the Flt-3 receptor, Hybridoma 17: 569-576; Schmolke et al., (1998) Identification of hepatitis G virus particles in human serum by E2-specific monoclonal antibodies generated by DNA immunization, J. Virol. 72: 4541-4545; Krasemann et al., (1999) Generation of monoclonal antibodies against proteins with an unconventional nucleic acid-based immunization strategy, J. Biotechnol. 73: 119-129; and Ulivieri et al., (1996) Generation of a monoclonal antibody to a defined portion of the Heliobacter pylori vacuolating cytotoxin by DNA immunization, J. Biotechnol. 51: 191-194, the disclosures of which are incorporated herein by reference in their entireties.

SOX7 and SOX18 are the closest Sox family relatives to SOX17 as depicted in the relational dendrogram shown in FIG. 3. We employed the human SOX7 polypeptide as a negative control to demonstrate that the SOX17 antibody is specific for SOX17 and does not react with its closest family member. In particular, to demonstrate that the antibody produced by genetic immunization is specific for SOX17, SOX7 and other proteins were expressed in human fibroblasts, and then, analyzed for cross reactivity with the SOX17 antibody by Western blot and ICC. For example, the following methods were utilized for the production of the SOX17, SOX7 and EGFP expression vectors, their transfection into human fibroblasts and analysis by Western blot. Expression vectors employed for the production of SOX17, SOX7, and EGFP were pCMV6 (OriGene Technologies, Inc., Rockville, Md.), pCMV-SPORT6 (Invitrogen, Carlsbad, Calif.) and pEGFP-N1 (Clonetech, Palo Alto, Calif.), respectively. For protein production, telomerase immortalized MDX human fibroblasts were transiently transfected with supercoiled DNA in the presence of Lipofectamine 2000 (Invitrogen, Carlsbad, Calif.). Total cellular lysates were collected 36 hours post-transfection in 50 mM TRIS-HCl (pH 8), 150 mM NaCl, 0.1% SDS, 0.5% deoxycholate, containing a cocktail of protease inhibitors (Roche Diagnostics Corporation, Indianapolis, Ind.). Western blot analysis of 100 μg of cellular proteins, separated by SDS-PAGE on NuPAGE (4-12% gradient polyacrylamide, Invitrogen, Carlsbad, Calif.), and transferred by electro-blotting onto PDVF membranes (Hercules, Calif.), were probed with a 1/1000 dilution of the rat SOX17 anti-serum in 10 mM TRIS-HCl (pH 8), 150 mM NaCl, 10% BSA, 0.05% Tween-20 (Sigma, St. Louis, Mo.), followed by Alkaline Phosphatase conjugated anti-rat IgG (Jackson ImmunoResearch Laboratories, West Grove, Pa.), and revealed through Vector Black Alkaline Phosphatase staining (Vector Laboratories, Burlingame, Calif.). The proteins size standard used was wide range color markers (Sigma, St. Louis, Mo.).

In FIG. 4, protein extracts made from human fibroblast cells that were transiently transfected with SOX17, SOX7 or EGFP cDNA's were probed on Western blots with the SOX17 antibody. Only the protein extract from hSOX17 transfected cells produced a band of ˜51 Kda which closely matched the predicted 46 Kda molecular weight of the human SOX17 protein. There was no reactivity of the SOX17 antibody to extracts made from either human SOX7 or EGFP transfected cells. Furthermore, the SOX17 antibody clearly labeled the nuclei of human fibroblast cells transfected with the hSOX17 expression construct but did not label cells transfected with EGFP alone. As such, the SOX17 antibody exhibits specificity by ICC.

Example 4 Validation of SOX17 Antibody as a Marker of Definitive Endoderm

As evidence that the SOX17 antibody is specific for human SOX17 protein and furthermore marks definitive endoderm, partially differentiated hESCs were co-labeled with SOX17 and AFP antibodies. It has been demonstrated that SOX17, SOX7, which is a closely related member of the SOX gene family subgroup F (FIG. 3), and AFP are each expressed in visceral endoderm. However, AFP and SOX7 are not expressed in definitive endoderm cells at levels detectable by ICC, and thus, they be can employed as negative markers for bonifide definitive endoderm cells. It was shown that SOX17 antibody labels populations of cells that exist as discrete groupings of cells or are intermingled with AFP positive cells. In particular, FIG. 5A shows that small numbers of SOX17 cells were co-labeled with AFP; however, regions were also found where there were little or no AFP⁺ cells in the field of SOX17⁺ cells (FIG. 5B). Similarly, since parietal endoderm has also been reported to express SOX17, antibody co-labeling with SOX17 together with the parietal markers SPARC and/or Thrombomodulin (TM) can be used to identify the SOX17⁺ cells which are parietal endoderm. As shown in FIGS. 6A-C, Thrombomodulin and SOX17 co-labelled parietal endoderm cells were produced by random differentiation of hES cells.

In view of the above cell labelling experiments, the identity of a definitive endoderm cell can be established by the marker profile SOX17^(hi)/AFP^(lo)/[TM^(lo) or SPARC^(lo)]. In other words, the expression of the SOX17 marker is greater than the expression of the AFP marker, which is characteristic of visceral endoderm, and the TM or SPARC markers, which are characteristic of parietal endoderm. Accordingly, those cells positive for SOX17 but negative for AFP and negative for TM or SPARC are definitive endoderm.

As a further evidence of the specificity of the SOX17^(hi)/AFP^(lo)/TM^(lo)/SPARC^(lo) marker profile as predictive of definitive endoderm, SOX17 and AFP gene expression was quantitatively compared to the relative number of antibody labeled cells. As shown in FIG. 7A, hESCs treated with retinoic acid (visceral endoderm inducer), or Activin A (definitive endoderm inducer), resulted in a 10-fold difference in the level of SOX17 mRNA expression. This result mirrored the 10-fold difference in SOX17 antibody-labeled cell number (FIG. 7B). Furthermore, as shown in FIG. 8A, Activin A treatment of hESCs suppressed AFP gene expression by 6.8-fold in comparison to no treatment. This was visually reflected by a dramatic decrease in the number of AFP labeled cells in these cultures as shown in FIGS. 8B-C. To quantify this further, it was demonstrated that this approximately 7-fold decrease in AFP gene expression was the result of a similar 7-fold decrease in AFP antibody-labeled cell number as measured by flow cytometry (FIGS. 9A-B). This result is extremely significant in that it indicates that quantitative changes in gene expression as seen by Q-PCR mirror changes in cell type specification as observed by antibody staining.

Incubation of hESCs in the presence of Nodal family members (Nodal, Activin A and Activin B-NAA) resulted in a significant increase in SOX17 antibody-labeled cells over time. By 5 days of continuous activin treatment greater than 50% of the cells were labeled with SOX17 (FIGS. 1A-F). There were few or no cells labeled with AFP after 5 days of activin treatment.

In summary, the antibody produced against the carboxy-terminal 242 amino acids of the human SOX17 protein identified human SOX17 protein on Western blots but did not recognize SOX7, it's closest Sox family relative. The SOX17 antibody recognized a subset of cells in differentiating HESC cultures that were primarily SOX17⁺/AFP^(lo/−) (greater than 95% of labeled cells) as well as a small percentage (<5%) of cells that co-label for SOX17 and AFP (visceral endoderm). Treatment of HESC cultures with activins resulted in a marked elevation of SOX17 gene expression as well as SOX17 labeled cells and dramatically suppressed the expression of AFP mRNA and the number of cells labeled with AFP antibody.

Example 5 Q-PCR Gene Expression Assay

In the following experiments, real-time quantitative RT-PCR (Q-PCR) was the primary assay used for screening the effects of various treatments on HESC differentiation. In particular, real-time measurements of gene expression were analyzed for multiple marker genes at multiple time points by Q-PCR. Marker genes characteristic of the desired as well as undesired cell types were evaluated to gain a better understanding of the overall dynamics of the cellular populations. The strength of Q-PCR analysis includes its extreme sensitivity and relative ease of developing the necessary markers, as the genome sequence is readily available. Furthermore, the extremely high sensitivity of Q-PCR permits detection of gene expression from a relatively small number of cells within a much larger population. In addition, the ability to detect very low levels of gene expression provides indications for “differentiation bias” within the population. The bias towards a particular differentiation pathway, prior to the overt differentiation of those cellular phenotypes, is unrecognizable using immunocytochemical techniques. For this reason, Q-PCR provides a method of analysis that is at least complementary and potentially much superior to immunocytochemical techniques for screening the success of differentiation treatments. Additionally, Q-PCR provides a mechanism by which to evaluate the success of a differentiation protocol in a quantitative format at semi-high throughput scales of analysis.

The approach taken here was to perform relative quantitation using SYBR Green chemistry on a Rotor Gene 3000 instrument (Corbett Research) and a two-step RT-PCR format. Such an approach allowed for the banking of cDNA samples for analysis of additional marker genes in the future, thus avoiding variability in the reverse transcription efficiency between samples.

Primers were designed to lie over exon-exon boundaries or span introns of at least 800 bp when possible, as this has been empirically determined to eliminate amplification from contaminating genomic DNA. When marker genes were employed that do not contain introns or they possess pseudogenes, DNase I treatment of RNA samples was performed.

We routinely used Q-PCR to measure the gene expression of multiple markers of target and non-target cell types in order to provide a broad profile description of gene expression in cell samples. The markers relevant for the early phases of hESC differentiation (specifically ectoderm, mesoderm, definitive endoderm and extra-embryonic endoderm) and for which validated primer sets are available are provided below in Table 1. The human specificity of these primer sets has also been demonstrated. This is an important fact since the hESCs were often grown on mouse feeder layers. Most typically, triplicate samples were taken for each condition and independently analyzed in duplicate to assess the biological variability associated with each quantitative determination.

To generate PCR template, total RNA was isolated using RNeasy (Qiagen) and quantitated using RiboGreen (Molecular Probes). Reverse transcription from 350-500 ng of total RNA was carried out using the iScript reverse transcriptase kit (BioRad), which contains a mix of oligo-dT and random primers. Each 20 μL reaction was subsequently diluted up to 100 μL total volume and 3 μL was used in each 10 μL Q-PCR reaction containing 400 nM forward and reverse primers and 5 μL 2×SYBR Green master mix (Qiagen). Two step cycling parameters were used employing a 5 second denature at 85-94° C. (specifically selected according to the melting temp of the amplicon for each primer set) followed by a 45 second anneal/extend at 60° C. Fluorescence data was collected during the last 15 seconds of each extension phase. A three point, 10-fold dilution series was used to generate the standard curve for each run and cycle thresholds (Ct's) were converted to quantitative values based on this standard curve. The quantitated values for each sample were normalized to housekeeping gene performance and then average and standard deviations were calculated for triplicate samples. At the conclusion of PCR cycling, a melt curve analysis was performed to ascertain the specificity of the reaction. A single specific product was indicated by a single peak at the T_(m) appropriate for that PCR amplicon. In addition, reactions performed without reverse transcriptase served as the negative control and do not amplify.

A first step in establishing the Q-PCR methodology was validation of appropriate housekeeping genes (HGs) in the experimental system. Since the HG was used to normalize across samples for the RNA input, RNA integrity and RT efficiency, it was of value that the HG exhibited a constant level of expression over time in all sample types in order for the normalization to be meaningful. We measured the expression levels of Cyclophilin G, hypoxanthine phosphoribosyltransferase 1 (HPRT), beta-2-microglobulin, hydroxymethylbiane synthase (HMBS), TATA-binding protein (TBP), and glucuronidase beta (GUS) in differentiating hESCs. Our results indicated that beta-2-microglobulin expression levels increased over the course of differentiation and therefore we excluded the use of this gene for normalization. The other genes exhibited consistent expression levels over time as well as across treatments. We routinely used both Cyclophilin G and GUS to calculate a normalization factor for all samples. The use of multiple HGs simultaneously reduces the variability inherent to the normalization process and increases the reliability of the relative gene expression values.

After obtaining genes for use in normalization, Q-PCR was then utilized to determine the relative gene expression levels of many marker genes across samples receiving different experimental treatments. The marker genes employed have been chosen because they exhibit enrichment in specific populations representative of the early germ layers and in particular have focused on sets of genes that are differentially expressed in definitive endoderm and extra-embryonic endoderm. These genes as well as their relative enrichment profiles are highlighted in Table 1.

TABLE 1 Germ Layer Gene Expression Domains Endoderm SOX17 definitive, visceral and parietal endoderm MIXL1 endoderm and mesoderm GATA4 definitive and primitive endoderm HNF3b definitive endoderm and primitive endoderm, mesoderm, neural plate GSC endoderm and mesoderm Extra- SOX7 visceral endoderm embryonic AFP visceral endoderm, liver SPARC parietal endoderm TM parietal endoderm/trophectoderm Ectoderm ZIC1 neural tube, neural progenitors Mesoderm BRACH nascent mesoderm

Since many genes are expressed in more than one germ layer it is useful to quantitatively compare expression levels of many genes within the same experiment. SOX17 is expressed in definitive endoderm and to a smaller extent in visceral and parietal endoderm. SOX7 and AFP are expressed in visceral endoderm at this early developmental time point. SPARC and TM are expressed in parietal endoderm and Brachyury is expressed in early mesoderm.

Definitive endoderm cells were predicted to express high levels of SOX17 mRNA and low levels of AFP and SOX7 (visceral endoderm), SPARC (parietal endoderm) and Brachyury (mesoderm). In addition, ZIC1 was used here to further rule out induction of early ectoderm. Finally, GATA4 and HNF3b were expressed in both definitive and extra-embryonic endoderm, and thus, correlate with SOX17 expression in definitive endoderm (Table 1). A representative experiment is shown in FIGS. 11-14 which demonstrates how the marker genes described in Table 1 correlate with each other among the various samples, thus highlighting specific patterns of differentiation to definitive endoderm and extra-embryonic endoderm as well as to mesodermal and neural cell types.

In view of the above data it is clear that increasing doses of activin resulted in increasing SOX17 gene expression. Further this SOX17 expression predominantly represented definitive endoderm as opposed to extra-embryonic endoderm. This conclusion stems from the observation that SOX17 gene expression was inversely correlated with AFP, SOX7, and SPARC gene expression.

Example 6 Directed Differentiation of Human ES Cells to Definitive Endoderm

Human ES cell cultures will randomly differentiate if they are cultured under conditions that do not actively maintain their undifferentiated state. This heterogeneous differentiation results in production of extra-embryonic endoderm cells comprised of both parietal and visceral endoderm (AFP, SPARC and SOX7 expression) as well as early ectodermal and mesodermal derivatives as marked by ZIC1 and Nestin (ectoderm) and Brachyury (mesoderm) expression. Definitive endoderm cell appearance has not traditionally been examined or specified for lack of specific antibody markers in ES cell cultures. As such, and by default, early definitive endoderm production in ES cell cultures has not been well studied. Since no good antibody reagents for definitive endoderm cells have been available, most of the characterization has focused on ectoderm and extra-embryonic endoderm. Overall, there are significantly greater numbers of extra-embryonic and neurectodermal cell types in comparison to SOX17^(hi) definitive endoderm cells in randomly differentiated ES cell cultures.

As undifferentiated HESC colonies expand on a bed of fibroblast feeders the edges of the colony take on alternative morphologies that are distinct from those cells residing within the interior of the colony. Many of these outer edge cells can be distinguished by their less uniform, larger cell body morphology and by the expression of higher levels of OCT4. It has been described that as ES cells begin to differentiate they alter the levels of OCT4 expression up or down relative to undifferentiated ES cells. Alteration of OCT4 levels above or below the undifferentiated threshold may signify the initial stages of differentiation away from the pluripotent state.

When undifferentiated colonies were examined by SOX17 immunocytochemistry, occasionally small 10-15-cell clusters of SOX17-positive cells were detected at random locations on the periphery and at the junctions between undifferentiated ESC colonies. As noted above, these scattered pockets of outer colony edges appeared to be some of the first cells to differentiate away from the classical ESC morphology as the colony expanded in size and became more crowded. Younger, smaller fully undifferentiated colonies (<1 mm; 4-5 days old) showed no SOX17 positive cells within or at the edges of the colonies while older, larger colonies (1-2 mm diameter, >5 days old) had sporadic isolated patches of SOX17 positive, AFP negative cells at the periphery of some colonies or in regions interior to the edge that were differentiated away from classical HESC morphology described previously. Given that this was the first development of an effective SOX17 antibody, definitive endoderm cells generated in such early “undifferentiated” ESC cultures have never been previously demonstrated.

Based on negative correlations of SOX17 and SPARC gene expression levels by Q-PCR, the vast majority of these SOX17 positive, AFP negative cells will be negative for parietal markers by antibody co-labeling. This was specifically demonstrated for TM-expressing parietal endoderm cells as shown in FIGS. 15A-B. Exposure to Nodal factors Activin A and B resulted in a dramatic decrease in the intensity to TM expression and the number of TM positive cells. By triple labeling using SOX17, AFP and TM antibodies on an activin treated culture, clusters of SOX17 positive cells which were also negative for AFP and TM were observed (FIGS. 16A-D). These are the first cellular demonstrations of SOX17 positive definitive endoderm cells in differentiating ESC cultures (FIGS. 16A-D and 17).

With the SOX17 antibody and Q-PCR tools described above we have explored a number of procedures capable of efficiently programming ESCs to become SOX17^(hi)/AFP^(lo)/SPARC/TM^(lo) definitive endoderm cells. We applied a variety of differentiation protocols aimed at increasing the number and proliferative capacity of these cells as measured at the population level by Q-PCR for SOX17 gene expression and at the level of individual cells by antibody labeling of SOX17 protein.

We were the first to analyze and describe the effect of TGFβ family growth factors, such as Nodal/activin/BMP, for use in creating definitive endoderm cells from embryonic stem cells in in vitro cell cultures. In typical experiments, Activin A, Activin B, BMP or combinations of these growth factors were added to cultures of undifferentiated human stem cell line hESCyt-25 to begin the differentiation process.

As shown in FIG. 19, addition of Activin A at 100 ng/ml resulted in a 19-fold induction of SOX17 gene expression vs. undifferentiated hESCs by day 4 of differentiation. Adding Activin B, a second member of the activin family, together with Activin A, resulted in a 37-fold induction over undifferentiated hESCs by day 4 of combined activin treatment. Finally, adding a third member of the TGFβ family from the Nodal/Activin and BMP subgroups, BMP4, together with Activin A and Activin B, increased the fold induction to 57 times that of undifferentiated hESCs (FIG. 19). When SOX17 induction with activins and BMP was compared to no factor medium controls 5-, 10-, and 15-fold inductions resulted at the 4-day time point. By five days of triple treatment with Activins A, B and BMP, SOX17 was induced more than 70 times higher than hESCs. These data indicate that higher doses and longer treatment times of the Nodal/activin TGFβ family members results in increased expression of SOX17.

Nodal and related molecules Activin A, B and BMP facilitate the expression of SOX17 and definitive endoderm formation in vivo or in vitro. Furthermore, addition of BMP results in an improved SOX17 induction possibly through the further induction of Cripto, the Nodal co-receptor.

We have demonstrated that the combination of Activins A and B together with BMP4 result in additive increases in SOX17 induction and hence definitive endoderm formation. BMP4 addition for prolonged periods (>4 days), in combination with Activin A and B may induce SOX17 in parietal and visceral endoderm as well as definitive endoderm. In some embodiments of the present invention, it is therefore valuable to remove BMP4 from the treatment within 4 days of addition.

To determine the effect of TGFβ factor treatment at the individual cell level, a time course of TGFβ factor addition was examined using SOX17 antibody labeling. As previously shown in FIGS. 10A-F, there was a dramatic increase in the relative number of SOX17 labeled cells over time. The relative quantitation (FIG. 20) shows more than a 20-fold increase in SOX17-labeled cells. This result indicates that both the numbers of cells as well SOX17 gene expression level are increasing with time of TGFβ factor exposure. As shown in FIG. 21, after four days of exposure to Nodal, Activin A, Activin B and BMP4, the level of SOX17 induction reached 168-fold over undifferentiated hESCs. FIG. 22 shows that the relative number of SOX17-positive cells was also dose responsive. Activin A doses of 100 ng/mL or more were capable of potently inducing SOX17 gene expression and cell number.

In addition to the TGFβ family members, the Wnt family of molecules may play a role in specification and/or maintenance of definitive endoderm. The use of Wnt molecules was also beneficial for the differentiation of hESCs to definitive endoderm as indicted by the increased SOX17 gene expression in samples that were treated with activins plus Wnt3a over that of activins alone (FIG. 23).

All of the experiments described above were performed using tissue culture medium containing 10% serum with added factors. Surprisingly, we discovered that the concentration of serum had an effect on the level of SOX17 expression in the presence of added activins as shown in FIGS. 24A-C. When serum levels were reduced from 10% to 2%, SOX17 expression tripled in the presence of Activins A and B.

Finally, we demonstrated that activin induced SOX17⁺ cells divide in culture as depicted in FIGS. 25A-D. The arrows show cells labeled with SOX17/PCNA/DAPI that are in mitosis as evidenced by the PCNA/DAPI-labeled mitotic plate pattern and the phase contrast mitotic profile.

Example 7 Chemokine Receptor 4 (CXCR4) Expression Correlates with Markers for Definitive Endoderm and not Markers for Mesoderm, Ectoderm or Visceral Endoderm

As described above, ESCs can be induced to differentiate to the definitive endoderm germ layer by the application of cytokines of the TGFβ family and more specifically of the activin/nodal subfamily. Additionally, we have shown that the proportion of fetal bovine serum (FBS) in the differentiation culture medium effects the efficiency of definitive endoderm differentiation from ESCs. This effect is such that at a given concentration of activin A in the medium, higher levels of FBS will inhibit maximal differentiation to definitive endoderm. In the absence of exogenous activin A, differentiation of ESCs to the definitive endoderm lineage is very inefficient and the FBS concentration has much milder effects on the differentiation process of ESCs.

In these experiments, hESCs were differentiated by growing in RPMI medium (Invitrogen, Carlsbad, Calif.; cat#61870-036) supplemented with 0.5%, 2.0% or 10% FBS and either with or without 100 ng/mL activin A for 6 days. In addition, a gradient of FBS ranging from 0.5% to 2.0% over the first three days of differentiation was also used in conjunction with 100 ng/mL of activin A. After the 6 days, replicate samples were collected from each culture condition and analyzed for relative gene expression by real-time quantitative PCR. The remaining cells were fixed for immunofluorescent detection of SOX17 protein.

The expression levels of CXCR4 varied dramatically across the 7 culture conditions used (FIG. 26). In general, CXCR4 expression was high in activin A treated cultures (A100) and low in those which did not receive exogenous activin A (NF). In addition, among the A100 treated cultures, CXCR4 expression was highest when FBS concentration was lowest. There was a remarkable decrease in CXCR4 level in the 10% FBS condition such that the relative expression was more in line with the conditions that did not receive activin A (NF).

As described above, expression of the SOX17, GSC, MIXL1, and HNF3β genes is consistent with the characterization of a cell as definitive endoderm. The relative expression of these four genes across the 7 differentiation conditions mirrors that of CXCR4 (FIGS. 27A-D). This demonstrates that CXCR4 is also a marker of definitive endoderm.

Ectoderm and mesoderm lineages can be distinguished from definitive endoderm by their expression of various markers. Early mesoderm expresses the genes Brachyury and MOX1 while nascent neuro-ectoderm expresses SOX1 and ZIC1. FIGS. 28A-D demonstrate that the cultures which did not receive exogenous activin A were preferentially enriched for mesoderm and ectoderm gene expression and that among the activin A treated cultures, the 10% FBS condition also had increased levels of mesoderm and ectoderm marker expression. These patterns of expression were inverse to that of CXCR4 and indicated that CXCR4 was not highly expressed in mesoderm or ectoderm derived from ESCs at this developmental time period.

Early during mammalian development, differentiation to extra-embryonic lineages also occurs. Of particular relevance here is the differentiation of visceral endoderm that shares the expression of many genes in common with definitive endoderm, including SOX17. To distinguish definitive endoderm from extra-embryonic visceral endoderm one should examine a marker that is distinct between these two. SOX7 represents a marker that is expressed in the visceral endoderm but not in the definitive endoderm lineage. Thus, culture conditions that exhibit robust SOX17 gene expression in the absence of SOX7 expression are likely to contain definitive and not visceral endoderm. It is shown in FIG. 28E that SOX7 was highly expressed in cultures that did not receive activin A, SOX7 also exhibited increased expression even in the presence of activin A when FBS was included at 10%. This pattern is the inverse of the CXCR4 expression pattern and suggests that CXCR4 is not highly expressed in visceral endoderm.

The relative number of SOX17 immunoreactive (SOX17⁺) cells present in each of the differentiation conditions mentioned above was also determined. When hESCs were differentiated in the presence of high dose activin A and low FBS concentration (0.5%-2.0%) SOX17⁺ cells were ubiquitously distributed throughout the culture. When high dose activin A was used but FBS was included at 10% (v/v), the SOX17⁺ cells appeared at much lower frequency and always appeared in isolated clusters rather than evenly distributed throughout the culture (FIGS. 29A and C as well as B and E). A further decrease in SOX17⁺ cells was seen when no exogenous activin A was used. Under these conditions the SOX17⁺ cells also appeared in clusters and these clusters were smaller and much more rare than those found in the high activin A, low FBS treatment (FIGS. 29 C and F). These results demonstrate that the CXCR4 expression patterns not only correspond to definitive endoderm gene expression but also to the number of definitive endoderm cells in each condition.

Example 8 Differentiation Conditions that Enrich for Definitive Endoderm Increase the Proportion of CXCR4 Positive Cells

The dose of activin A also effects the efficiency at which definitive endoderm can be derived from ESCs. This example demonstrates that increasing the dose of activin A increases the proportion of CXCR4⁺ cells in the culture.

hESCs were differentiated in RPMI media supplemented with 0.5%-2% FBS (increased from 0.5% to 1.0% to 2.0% over the first 3 days of differentiation) and either 0, 10, or 100 ng/mL of activin A. After 7 days of differentiation the cells were dissociated in PBS without Ca²⁺/Mg²⁺ containing 2% FBS and 2 mM (EDTA) for 5 minutes at room temperature. The cells were filtered through 35 um nylon filters, counted and pelleted. Pellets were resuspended in a small volume of 50% human serum/50% normal donkey serum and incubated for 2 minutes on ice to block non-specific antibody binding sites. To this, 1 uL of mouse anti-CXCR4 antibody (Abeam, cat# ab10403-100) was added per 50 uL (containing approximately 10⁵ cells) and labeling proceeded for 45 minutes on ice. Cells were washed by adding 5 mL of PBS containing 2% human serum (buffer) and pelleted. A second wash with 5 mL of buffer was completed then cells were resuspended in 50 uL buffer per 10⁵ cells. Secondary antibody (FITC conjugated donkey anti-mouse; Jackson ImmunoResearch, cat#715-096-151) was added at 5 ug/mL final concentration and allowed to label for 30 minutes followed by two washes in buffer as above. Cells were resuspended at 5×10⁶ cells/mL in buffer and analyzed and sorted using a FACS Vantage (Beckton Dickenson) by the staff at the flow cytometry core facility (The Scripps Research Institute). Cells were collected directly into RLT lysis buffer (Qiagen) for subsequent isolation of total RNA for gene expression analysis by real-time quantitative PCR.

The number of CXCR4⁺ cells as determined by flow cytometry were observed to increase dramatically as the dose of activin A was increased in the differentiation culture media (FIGS. 30A-C). The CXCR4⁺ cells were those falling within the R4 gate and this gate was set using a secondary antibody-only control for which 0.2% of events were located in the R4 gate. The dramatically increased numbers of CXCR4⁺ cells correlates with a robust increase in definitive endoderm gene expression as activin A dose is increased (FIGS. 31A-D).

Example 9 Isolation of CXCR4 Positive Cells Enriches for Definitive Endoderm Gene Expression and Depletes Cells Expressing Markers of Mesoderm, Ectoderm and Visceral Endoderm

The CXCR4⁺ and CXCR4⁻ cells identified in Example 8 above were collected and analyzed for relative gene expression and the gene expression of the parent populations was determined simultaneously.

The relative levels of CXCR4 gene expression was dramatically increased with increasing dose of activin A (FIG. 32). This correlated very well with the activin A dose-dependent increase of CXCR4⁺ cells (FIGS. 30A-C). It is also clear that isolation of the CXCR4⁺ cells from each population accounted for nearly all of the CXCR4 gene expression in that population. This demonstrates the efficiency of the FACS method for collecting these cells.

Gene expression analysis revealed that the CXCR4⁺ cells contain not only the majority of the CXCR4 gene expression, but they also contained other gene expression for markers of definitive endoderm. As shown in FIGS. 31A-D, the CXCR4⁺ cells were further enriched over the parent A100 population for SOX17, GSC, HNF3B, and MIXL1. In addition, the CXCR4⁻ fraction contained very little gene expression for these definitive endoderm markers. Moreover, the CXCR4⁺ and CXCR4⁻ populations displayed the inverse pattern of gene expression for markers of mesoderm, ectoderm and extra-embryonic endoderm. FIGS. 33A-D shows that the CXCR4⁺ cells were depleted for gene expression of Brachyury, MOX1, ZIC1, and SOX7 relative to the A100 parent population. This A100 parent population was already low in expression of these markers relative to the low dose or no activin A conditions. These results show that the isolation of CXCR4⁺ cells from hESCs differentiated in the presence of high activin A yields a population that is highly enriched for and substantially pure definitive endoderm.

Example 10 Quantitation of Definitive Endoderm Cells in a Cell Population Using CXCR4

To confirm the quantitation of the proportion of definitive endoderm cells present in a cell culture or cell population as determined previously herein and as determined in U.S. Provisional Patent Application No. 60/532,004, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2003, the disclosure of which is incorporated herein by reference in its entirety, cells expressing CXCR4 and other markers of definitive endoderm were analyzed by FACS.

Using the methods such as those described in the above Examples, hESCs were differentiated to produce definitive endoderm. In particular, to increase yield and purity expressed in differentiating cell cultures, the serum concentration of the medium was controlled as follows: 0.2% FBS on day 1, 1.0% FBS on day 2 and 2.0% FBS on days 3-6. Differentiated cultures were sorted by FACS using three cell surface epitopes, E-Cadherin, CXCR4, and Thrombomodulin. Sorted cell populations were then analyzed by Q-PCR to determine relative expression levels of markers for definitive and extraembryonic-endoderm as well as other cell types. CXCR4 sorted cells taken from optimally differentiated cultures resulted in the isolation of definitive endoderm cells that were >98% pure.

Table 2 shows the results of a marker analysis for a definitive endoderm culture that was differentiated from hESCs using the methods described herein.

TABLE 2 Composition of Definitive Endoderm Cultures Percent Percent Percent ercent of Definitive Extraembryonic hES Marker(s) culture Endoderm endododerm cells SOX17 70-80 100 Thrombomodulin <2 0 75 AFP <1 0 25 CXCR4 70-80 100 0 ECAD 10 0 100 other (ECAD neg.) 10-20 Total 100 100 100 100

In particular, Table 2 indicates that CXCR4 and SOX17 positive cells (endoderm) comprised from 70%-80% of the cells in the cell culture. Of these SOX17-expressing cells, less than 2% expressed TM (parietal endoderm) and less than 1% expressed AFP (visceral endoderm). After subtracting the proportion of TM-positive and AFP-positive cells (combined parietal and visceral endoderm; 3% total) from the proportion of SOX17/CXCR4 positive cells, it can be seen that about 67% to about 77% of the cell culture was definitive endoderm. Approximately 10% of the cells were positive for E-Cadherin (ECAD), which is a marker for hESCs, and about 10-20% of the cells were of other cell types.

We have discovered that the purity of definitive endoderm in the differentiating cell cultures that are obtained prior to FACS separation can be improved as compared to the above-described low serum procedure by maintaining the FBS concentration at ≦0.5% throughout the 5-6 day differentiation procedure. However, maintaining the cell culture at ≦0.5% throughout the 5-6 day differentiation procedure also results in a reduced number of total definitive endoderm cells that are produced.

Definitive endoderm cells produced by methods described herein have been maintained and expanded in culture in the presence of activin for greater than 50 days without appreciable differentiation. In such cases, SOX17, CXCR4, MIXL1, GATA4, HNF3β expression is maintained over the culture period. Additionally, TM, SPARC, OCT4, AFP, SOX7, ZIC1 and BRACH were not detected in these cultures. It is likely that such cells can be maintained and expanded in culture for substantially longer than 50 days without appreciable differentiation.

Example 11 Additional Markers of Definitive Endoderm Cells

In the following experiment, RNA was isolated from purified definitive endoderm and human embryonic stem cell populations. Gene expression was then analyzed by gene chip analysis of the RNA from each purified population. Q-PCR was also performed to further investigate the potential of genes expressed in definitive endoderm, but not in embryonic stem cells, as a marker for definitive endoderm.

Human embryonic stem cells (hESCs) were maintained in DMEM/F12 media supplemented with 20% KnockOut Serum Replacement, 4 ng/mL recombinant human basic fibroblast growth factor (bFGF), 0.1 mM 2-mercaptoethanol, L-glutamine, non-essential amino acids and penicillin/streptomycin. hESCs were differentiated to definitive endoderm by culturing for 5 days in RPMI media supplemented with 100 ng/mL of recombinant human activin A, fetal bovine serum (FBS), and penicillin/streptomycin. The concentration of FBS was varied each day as follows: 0.1% (first day), 0.2% (second day), 2% (days 3-5).

Cells were isolated by fluorescence activated cell sorting (FACS) in order to obtain purified populations of hESCs and definitive endoderm for gene expression analysis. Immuno-purification was achieved for hESCs using SSEA4 antigen (R&D Systems, cat# FAB1435P) and for definitive endoderm using CXCR4 (R&D Systems, cat# FAB170P). Cells were dissociated using trypsin/EDTA (Invitrogen, cat#25300-054), washed in phosphate buffered saline (PBS) containing 2% human serum and resuspended in 100% human serum on ice for 10 minutes to block non-specific binding. Staining was carried out for 30 minutes on ice by adding 200 uL of phycoerythrin-conjugated antibody to 5×10⁶ cells in 800 uL human serum. Cells were washed twice with 8 mL of PBS buffer and resuspended in 1 mL of the same. FACS isolation was carried out by the core facility of The Scripps Research Institute using a FACS Vantage (BD Biosciences). Cells were collected directly into RLT lysis buffer and RNA was isolated by RNeasy according to the manufacturers instructions (Qiagen).

Purified RNA was submitted in duplicate to Expression Analysis (Durham, N.C.) for generation of the expression profile data using the Affymetrix platform and U133 Plus 2.0 high-density oligonucleotide arrays. Data presented is a group comparison that identifies genes differentially expressed between the two populations, hESCs and definitive endoderm.

Genes that exhibited an upward change in expression level over that found in hESCs are described in Table 3. The “Gene_Symbol” column refers to the unique name given to the gene by the HUGO Gene Nomenclature Committee. The “Raw Fold Change” column refers to the fold difference in signal for each gene in definitive endoderm compared to hESCs. The “Unigene,” “LocusLink,” and “OMIM” columns refer to identifiers that are descriptive and functional annotations derived from current National Center for Biotechnology Information (NCBI) releases of the UniGene, LocusLink, OMIM, and HomoloGene publicly available databases. The column entitled “SeqDerivedFrom” provides the Genbank Accession Number for a primary database sequence, such as a fragment of a chromosome, from which the listed gene was derived. The column entitled “Gene Descriptor” provides a description of the function of the polypeptide that is encoded by the gene named in the first column.

TABLE 3 Up-regulated markers in definitive endoderm Raw Fold Gene_Symbol Change Unigene LocusLink OMIM SeqDerivedFrom Gene Descriptor ABCB4 5.22 Hs.73812 5244 171060 BC020618 ATP-binding cassette, sub-family B (MDR/TAP), member 4 ABCC4 7.18 Hs.307915 10257 605250 AI948503 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 ABI2 5.95 Hs.387906 10152 606442 AF070566 abl interactor 2 ACADL 7.09 Hs.430108 33 201460 NM_001608 acyl-Coenzyme A dehydrogenase, long chain ACE2 26.83 Hs.178098 59272 300335 NM_021804 angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 ACOX3 13.04 Hs.12773 8310 603402 BF055171 acyl-Coenzyme A oxidase 3, pristanoyl ACPP 7.06 Hs.388677 55 171790 AI659898 acid phosphatase, prostate ACSL1 14.73 Hs.406678 2180 152425 NM_021122 acyl-CoA synthetase long-chain family member 1 ACSL3 6.01 Hs.268012 2181 602371 BF512846 acyl-CoA synthetase long-chain family member 3 ACTA1 8.03 Hs.1288 58 102610 NM_001100 actin, alpha 1, skeletal muscle ADAM19 6.68 Hs.289368 8728 603640 Y13786 a disintegrin and metalloproteinase domain 19 (meltrin beta) ADAMTS18 17.65 Hs.188746 170692 607512 AI733120 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18 ADAMTS9 16.19 Hs.318751 56999 605421 AF488803 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9 ADRA1B 5.21 Hs.416813 147 104220 NM_000679 adrenergic, alpha-1B-, receptor AGPAT3 53.81 Hs.443657 56894 AI337300 1-acylglycerol-3-phosphate O-acyltransferase 3 AHI1 6.21 Hs.273294 54806 AV658469 Abelson helper integration site AIP1 6.21 Hs.22599 9863 606382 NM_012301 atrophin-1 interacting protein 1 ALAD 5.43 Hs.1227 210 125270 BC000977 aminolevulinate, delta-, dehydratase AMHR2 9.46 Hs.437877 269 600956 NM_020547 anti-Mullerian hormone receptor, type II ANGPT2 13.75 Hs.115181 285 601922 NM_001147 angiopoietin 2 ANGPTL1 6.19 Hs.304398 9068 603874 BF002046 angiopoietin-lik 1 ANK2 10.11 Hs.409783 287 106410 AF131823 ankyrin 2, neuronal ANKH 26.52 Hs.156727 56172 605145 NM_019847 ankylosis, progressive homolog (mouse) ANKRD6 14.01 Hs.30991 22881 NM_014942 ankyrin repeat domain 6 ANXA3 5.06 Hs.442733 306 106490 M63310 annexin A3 APC 6.40 Hs.75081 324 175100 NM_000038 adenomatosis polyposis coli APOA1 15.05 Hs.93194 335 107680 X02162 apolipoprotein A-I APOA2 33.51 Hs.237658 336 107670 NM_001643 apolipoprotein A-II APOBEC3G 15.76 Hs.286849 60489 607113 NM_021822 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G APOC1 5.13 Hs.268571 341 107710 NM_001645 apolipoprotein C-I APOL3 5.88 Hs.241535 80833 607253 NM_014349 apolipoprotein L, 3 ARF4L 15.64 Hs.183153 379 600732 NM_001661 ADP-ribosylation factor 4-like ARG99 5.44 Hs.528689 83857 AU151239 ARG99 protein ARHGAP18 18.34 Hs.413282 93663 AU158022 Rho GTPase activating protein 18 ARHGAP24 10.96 Hs.442801 83478 AI743534 Rho GTPase activating protein 24 ARHGEF4 5.19 Hs.6066 50649 605216 NM_015320 Rho guanine nucleotide exchange factor (GEF) 4 ARHGEF7 5.10 Hs.172813 8874 605477 AL831814 Rho guanine nucleotide exchange factor (GEF) 7 ARK5 8.63 Hs.200598 9891 608130 NM_014840 AMP-activated protein kinase family member 5 ARMCX1 5.24 Hs.9728 51309 300362 NM_016608 armadillo repeat containing, X-linked 1 ARRB1 13.03 Hs.112278 408 107940 NM_004041 arrestin, beta 1 ARSE 7.26 Hs.386975 415 300180 NM_000047 arylsulfatase E (chondrodysplasia punctata 1) ASAM 7.31 Hs.135121 79827 BG112263 adipocyte-specific adhesion molecule ASB4 10.03 Hs.413226 51666 605761 BE220587 ankyrin repeat and SOCS box-containing 4 ASB5 47.32 Hs.352364 140458 BF589787 ankyrin repeat and SOCS box-containing 5 AUTS2 13.27 Hs.296720 26053 607270 AI417756 autism susceptibility candidate 2 BCAR3 5.47 Hs.201993 8412 604704 NM_003567 breast cancer anti-estrogen resistance 3 BCAT2 7.68 Hs.512670 587 113530 AK023909 branched chain aminotransferase 2, mitochondrial BCL2L14 8.79 Hs.11962 79370 606126 AI554912 BCL2-like 14 (apoptosis facilitator) BCL7C 7.80 Hs.303197 9274 605847 NM_004765 B-cell CLL/lymphoma 7C BHLHB5 7.16 Hs.388788 27319 AL134708 basic helix-loop-helix domain containing, class B, 5 BIRC3 7.41 Hs.127799 330 601721 U37546 baculoviral IAP repeat-containing 3 BMP2 7.76 Hs.73853 650 112261 NM_001200 bone morphogenetic protein 2 BMPER 5.53 Hs.71730 168667 608699 AI423201 BMP-binding endothelial regulator precursor protein BMPR2 6.05 Hs.53250 659 600799 AI457436 bone morphogenetic protein receptor, type II (serine/threonine kinase) BRUNOL4 10.60 Hs.435976 56853 AI697701 bruno-like 4, RNA binding protein (Drosophila) BSPRY 6.56 Hs.108502 54836 NM_017688 B-box and SPRY domain containing BTG2 5.88 Hs.75462 7832 601597 NM_006763 BTG family, member 2 BTK 5.13 Hs.159494 695 300300 NM_000061 Bruton agammaglobulinemia tyrosine kinase C10orf39 9.09 Hs.106254 282973 AL137551 chromosome 10 open reading frame 39 C10orf94 12.58 Hs.311003 93426 BC034821 chromosome 10 open reading frame 94 C11orf21 5.13 Hs.272100 29125 BM547346 chromosome 11 open reading frame 21 C13orf25 7.13 407975 AF339828 chromosome 13 open reading frame 25 C14orf139 13.95 Hs.41502 79686 NM_024633 chromosome 14 open reading frame 139 C18orf1 5.05 Hs.285091 753 606571 AW008505 chromosome 18 open reading frame 1 C18orf14 17.69 Hs.146025 79839 NM_024781 chromosome 18 open reading frame 14 C20orf56 36.01 140828 AL121722 chromosome 20 open reading frame 56 C21orf105 10.03 Hs.386685 90625 BC005107 chromosome 21 open reading frame 105 C21orf129 77.87 Hs.350679 150135 NM_152506 chromosome 21 open reading frame 129 C21orf2 6.17 Hs.155361 755 603191 U84569 chromosome 21 open reading frame 2 C21orf29 5.57 Hs.473997 54084 BC021197 chromosome 21 open reading frame 29 C21orf30 6.67 Hs.222909 54083 AL117578 chromosome 21 open reading frame 30 C5 15.16 Hs.1281 727 120900 NM_001735 complement component 5 C5orf13 6.29 Hs.508741 9315 607332 AI733949 chromosome 5 open reading frame 13 C6orf164 9.47 63914 NM_022084 chromosome 6 open reading frame 164 C6orf182 11.05 Hs.375746 285753 BE567344 chromosome 6 open reading frame 182 C6orf4 6.58 Hs.437508 10758 607043 AI916498 chromosome 6 open reading frame 4 C6orf52 9.39 347744 AW103116 chromosome 6 open reading frame 52 C6orf54 6.13 Hs.225962 26236 AB016900 chromosome 6 open reading frame 54 C6orf60 21.05 Hs.20537 79632 AJ420563 chromosome 6 open reading frame 60 C6orf97 5.47 Hs.287738 80129 NM_025059 chromosome 6 open reading frame 97 C8orf13 8.66 Hs.318791 83648 BE856336 chromosome 8 open reading frame 13 C8orf6 7.04 Hs.291342 203081 NM_145656 chromosome 8 open reading frame 6 C9orf154 22.03 Hs.119947 158326 AI824037 chromosome 9 open reading frame 154 C9orf52 10.19 Hs.49605 158219 AW001030 chromosome 9 open reading frame 52 C9orf64 12.97 Hs.208914 84267 AW983691 chromosome 9 open reading frame 64 C9orf66 8.78 Hs.190877 157983 NM_152569 chromosome 9 open reading frame 66 C9orf71 7.44 Hs.96641 169693 AW271796 chromosome 9 open reading frame 71 CALB1 11.26 Hs.65425 793 114050 NM_004929 calbindin 1, 28 kDa CALCR 38.31 Hs.640 799 114131 NM_001742 calcitonin receptor CAMK2D 7.15 Hs.111460 817 607708 BF797381 calcium/calmodulin-dependent protein kinase (CaM kinase) II delta CAP2 5.83 Hs.296341 10486 N90755 CAP, adenylate cyclase-associated protein, 2 (yeast) CASK 9.64 Hs.288196 8573 300172 AI659225 calcium/calmodulin-dependent serine protein kinase (MAGUK family) CASP1 9.90 Hs.2490 834 147678 AI719655 caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase) CBLB 5.96 Hs.436986 868 604491 NM_004351 Cas-Br-M (murine) ecotropic retroviral transforming sequence b CCKBR 27.45 Hs.203 887 118445 BC000740 cholecystokinin B receptor CCL2 111.46 Hs.303649 6347 158105 S69738 chemokine (C-C motif) ligand 2 CCR4 5.70 Hs.506129 1233 604836 NM_005508 chemokine (C-C motif) receptor 4 CD163 9.73 Hs.74076 9332 605545 Z22969 CD163 antigen CD44 5.25 Hs.306278 960 107269 AW851559 CD44 antigen (homing function and Indian blood group system) CD80 8.85 Hs.838 941 112203 AY081815 CD80 antigen (CD28 antigen ligand 1, B7-1 antigen) CD99 5.86 Hs.283477 4267 313470/ U82164 CD99 antigen CDGAP 10.17 Hs.300670 57514 AB033030 KIAA1204 protein CDH12 9.44 Hs.333997 1010 600562 L33477 cadherin 12, type 2 (N-cadherin 2) CDH2 8.85 Hs.334131 1000 114020 NM_001792 cadherin 2, type 1, N-cadherin (neuronal) CDK5R2 5.13 Hs.158460 8941 603764 R51311 cyclin-dependent kinase 5, regulatory subunit 2 (p39) CDKN2B 8.45 Hs.72901 1030 600431 AW444761 cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) CDW92 5.10 Hs.414728 23446 606105 AW444881 CDW92 antigen CER1 33.04 Hs.248204 9350 603777 NM_005454 cerberus 1 homolog, cysteine knot superfamily (Xenopus laevis) CFLAR 21.93 Hs.355724 8837 603599 AF005775 CASP8 and FADD-like apoptosis regulator CFTR 5.50 Hs.411882 1080 602421 S64699 cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7) CGI-38 19.67 Hs.412685 51673 NM_016140 brain specific protein CLDN1 7.32 Hs.7327 9076 603718 AF101051 claudin 1 CLDN11 7.86 Hs.31595 5010 601326 AW264204 claudin 11 (oligodendrocyte transmembrane protein) CMKOR1 53.39 Hs.231853 57007 AI817041 chemokine orphan receptor 1 CNTN3 7.56 Hs.512593 5067 601325 BE221817 contactin 3 (plasmacytoma associated) CNTN4 5.13 Hs.121115 152330 607280 R42166 contactin 4 COL22A1 5.12 Hs.116394 169044 BE349115 collagen, type XXII, alpha 1 COL4A3 9.58 Hs.407817 1285 120070 AI694562 collagen, type IV, alpha 3 (Goodpasture antigen) COL5A2 6.62 Hs.283393 1290 120190 NM_000393 collagen, type V, alpha 2 COL8A1 11.41 Hs.114599 1295 120251 AL359062 collagen, type VIII, alpha 1 COL9A2 7.94 Hs.418012 1298 120260 AI733465 collagen, type IX, alpha 2 COLEC12 24.49 Hs.29423 81035 607621 NM_030781 collectin sub-family member 12 CPE 13.90 Hs.75360 1363 114855 NM_001873 carboxypeptidase E CPXCR1 5.03 Hs.458292 53336 AK098646 CPX chromosome region, candidate 1 CRIP1 50.56 1396 123875 NM_001311 cysteine-rich protein 1 (intestinal) CST1 6.20 Hs.123114 1469 123855 NM_001898 cystatin SN CTSH 5.20 Hs.114931 1512 116820 NM_004390 cathepsin H CXCR4 55.31 Hs.421986 7852 162643 AJ224869 chemokine (C—X—C motif) receptor 4 CXorf1 54.35 Hs.106688 9142 NM_004709 chromosome X open reading frame 1 CYLC1 11.56 Hs.444230 1538 603121 Z22780 cylicin, basic protein of sperm head cytoskeleton 1 CYP27A1 19.84 Hs.82568 1593 606530 NM_000784 cytochrome P450, family 27, subfamily A, polypeptide 1 DACT2 11.72 Hs.248294 168002 AF318336 dapper homolog 2, antagonist of beta-catenin (xenopus) DDC 8.62 Hs.408106 1644 107930 NM_000790 dopa decarboxylase (aromatic L-amino acid decarboxylase) DDIT4L 5.33 Hs.107515 115265 607730 AA528140 DNA-damage-inducible transcript 4-like DIO3 33.07 Hs.49322 1735 601038 NM_001362 deiodinase, iodothyronine, type III DIO3OS 59.10 Hs.406958 64150 608523 AF305836 deiodinase, iodothyronine, type III opposite strand DIRAS2 8.07 Hs.165636 54769 607863 NM_017594 DIRAS family, GTP-binding RAS-like 2 dJ222E13.1 28.34 Hs.301947 253190 AL590118 kraken-like DKFZp434C184 5.73 Hs.531492 399474 N63821 cDNA DKFZp434C184 gene DKFZp564I1922 6.26 Hs.72157 25878 AF245505 adlican DKFZp566F0947 7.27 Hs.220597 94023 AL137518 hypothetical gene DKFZp566F0947 DKFZP586M1120 5.29 Hs.159068 83450 BC040276 hypothetical protein DKFZp586M1120 DLC1 13.62 Hs.8700 10395 604258 AA524250 deleted in liver cancer 1 DLEC1 9.06 Hs.277589 9940 604050 NM_007337 deleted in lung and esophageal cancer 1 DLEU2 8.62 Hs.446406 8847 605766 AF264787 deleted in lymphocytic leukemia, 2 DLG5 5.88 Hs.500245 9231 604090 AI809998 discs, large homolog 5 (Drosophila) DNAH14 7.14 Hs.381271 1772 603341 U61741 dynein, axonemal, heavy polypeptide 14 DNAJC6 9.80 Hs.129587 9829 608375 AV729634 DnaJ (Hsp40) homolog, subfamily C, member 6 DNAJD1 6.48 Hs.438830 29103 NM_013238 DnaJ (Hsp40) homolog, subfamily D, member 1 DNMT3L 14.53 Hs.157237 29947 606588 NM_013369 DNA (cytosine-5-)-methyltransferase 3-like DOCK5 5.24 Hs.383002 80005 AL832744 dedicator of cytokinesis 5 DOCK8 16.36 Hs.528687 81704 AL161725 dedicator of cytokinesis 8 DPYD 33.20 Hs.1602 1806 274270 NM_000110 dihydropyrimidine dehydrogenase DSCAM 8.25 Hs.49002 1826 602523 BE503065 Down syndrome cell adhesion molecule DSCAML1 5.56 Hs.397966 57453 AK025940 Down syndrome cell adhesion molecule like 1 DSCR6 21.62 Hs.254560 53820 NM_018962 Down syndrome critical region gene 6 DUSP4 22.18 Hs.417962 1846 602747 NM_001394 dual specificity phosphatase 4 EB-1 162.04 Hs.372732 56899 607815 AW005572 E2a-Pbx1-associated protein EBAF 14.86 Hs.25195 7044 601877 NM_003240 endometrial bleeding associated factor (left-right determination, factor A; transforming growth factor beta superfamily) EBI2 5.68 Hs.784 1880 605741 NM_004951 Epstein-Barr virus induced gene 2 (lymphocyte-Specific G protein-coupled receptor) ED1 8.13 Hs.105407 1896 300451 NM_001399 ectodermal dysplasia 1, anhidrotic EDG3 20.71 Hs.353892 1903 601965 NM_005226 endothelial differentiation, sphingolipid G-protein-coupled receptor, 3 EDG3 12.22 Hs.4257 1903 601965 AA534817 endothelial differentiation, sphingolipid G-protein-coupled receptor, 3 EDNRA 5.58 Hs.211202 1909 131243 AU118882 endothelin receptor type A EGF 13.71 Hs.419815 1950 131530 NM_001963 epidermal growth factor (beta-urogastrone) EHHADH 85.52 Hs.432443 1962 607037 NM_001966 enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase EIF5A2 5.20 Hs.164144 56648 605782 AV747725 eukaryotic translation initiation factor 5A2 ELMO1 7.28 Hs.444695 9844 606420 NM_014800 engulfment and cell motility 1 (ced-12 homolog, C. elegans) ELOVL2 70.71 Hs.246107 54898 BF508639 elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2 EMR2 5.66 Hs.137354 30817 606100 NM_013447 egf-like module containing, mucin-like, hormone receptor-like 2 ENPEP 10.17 Hs.435765 2028 138297 L12468 glutamyl aminopeptidase (aminopeptidase A) EOMES 16.02 Hs.147279 8320 604615 NM_005442 eomesodermin homolog (Xenopus laevis) EPHB3 8.99 Hs.2913 2049 601839 NM_004443 EphB3 EPOR 6.92 Hs.127826 2057 133171 BU727288 erythropoietin receptor EPSTI1 34.25 Hs.343800 94240 607441 AA633203 epithelial stromal interaction 1 (breast) ERBB4 6.35 Hs.1939 2066 600543 NM_005235 v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) ERO1LB 5.94 Hs.424926 56605 NM_019891 ERO1-like beta (S. cerevisiae) ETS2 6.96 Hs.292477 2114 164740 AL575509 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) EVC 26.80 Hs.28051 2121 604831 NM_014556 Ellis van Creveld syndrome FAM13C1 5.24 Hs.311205 220965 BC036453 family with sequence similarity 13, member C1 FAM38B 5.63 Hs.293907 63895 AW269818 family with sequence similarity 38, member B FANK1 9.17 Hs.352591 92565 AU143929 fibronectin type 3 and ankyrin repeat domains 1 FBS1 7.33 Hs.247186 64319 608601 AW134523 fibrosin 1 FBXL14 7.12 Hs.367956 144699 NM_152441 F-box and leucine-rich repeat protein 14 FBXL8 10.33 Hs.75486 55336 NM_018378 F-box and leucine-rich repeat protein 8 FBXO32 5.70 Hs.403933 114907 606604 BF244402 F-box only protein 32 FBXO4 6.29 Hs.437345 26272 NM_018007 F-box only protein 4 FCGR2A 6.65 Hs.352642 2212 146790 AF416711 Fc fragment of IgG, low affinity IIa, receptor for (CD32) FER1L3 15.13 Hs.362731 26509 604603 AF207990 fer-1-like 3, myoferlin (C. elegans) FES 9.36 Hs.7636 2242 190030 NM_002005 feline sarcoma oncogene FGD6 5.11 Hs.170623 55785 AK026881 FYVE, RhoGEF and PH domain containing 6 FGF17 107.07 Hs.248192 8822 603725 NM_003867 fibroblast growth factor 17 FGF8 14.46 Hs.57710 2253 600483 NM_006119 fibroblast growth factor 8 (androgen-induced) FKBP9 5.00 Hs.497972 11328 AL050187 FK506 binding protein 9, 63 kDa FLJ10312 30.88 Hs.183114 79822 NM_030672 hypothetical protein FLJ10312 FLJ10970 50.86 Hs.173233 55273 NM_018286 hypothetical protein FLJ10970 FLJ10996 10.14 Hs.98324 54520 AA504256 hypothetical protein FLJ10996 FLJ11082 8.96 Hs.31792 55296 NM_018317 hypothetical protein FLJ11082 FLJ11155 9.25 Hs.176227 55314 AW173720 hypothetical protein FLJ11155 FLJ11175 5.55 Hs.33368 55784 AI052257 hypothetical protein FLJ11175 FLJ11506 5.76 Hs.254642 79719 AL136715 hypothetical protein FLJ11506 FLJ12476 16.70 Hs.88144 64799 NM_022784 hypothetical protein FLJ12476 FLJ13231 8.43 Hs.156148 65250 NM_023073 hypothetical protein FLJ13231 FLJ13330 6.67 Hs.193048 80161 NM_025091 hypothetical protein FLJ13330 FLJ13373 6.74 Hs.494757 387751 AL833700 very large inducible GTPase 1 FLJ13725 5.66 Hs.152717 79567 NM_024519 hypothetical protein FLJ13725 FLJ14721 5.09 Hs.144655 84915 BE551088 hypothetical protein FLJ14721 FLJ20014 13.09 Hs.129563 54785 NM_017622 hypothetical protein FLJ20014 FLJ20265 5.65 Hs.7099 54872 AV650183 hypothetical protein FLJ20265 FLJ20489 5.47 Hs.438867 55652 AW149696 hypothetical protein FLJ20489 FLJ21069 10.30 Hs.341806 79745 NM_024692 hypothetical protein FLJ21069 FLJ21195 83.56 Hs.207407 64388 BF064262 protein related to DAN and cerberus FLJ22028 5.58 Hs.192570 79912 AI554909 hypothetical protein FLJ22028 FLJ22471 34.33 Hs.387266 80212 NM_025140 limkain beta 2 FLJ22527 34.12 Hs.113009 79781 W52934 hypothetical protein FLJ22527 FLJ23091 7.90 Hs.297792 79971 AL534095 putative NFkB activating protein 373 FLJ23514 46.65 Hs.144913 60494 NM_021827 hypothetical protein FLJ23514 FLJ23554 5.34 Hs.164705 79864 NM_024806 hypothetical protein FLJ23554 FLJ25348 6.51 Hs.62604 90853 AK096192 hypothetical protein FLJ25348 FLJ30672 5.97 158696 NM_153016 hypothetical protein FLJ30672 FLJ31842 21.12 Hs.84522 148534 AI004375 hypothetical protein FLJ31842 FLJ32949 5.81 Hs.484250 283417 AA758751 hypothetical protein FLJ32949 FLJ34222 5.82 284350 AA180985 hypothetical protein FLJ34222 FLJ36004 5.56 Hs.369235 160492 NM_152590 hypothetical protein FLJ36004 FLJ37451 15.44 Hs.153485 284161 R46180 hypothetical protein FLJ37451 FLJ39502 16.72 Hs.99104 285025 NM_173648 hypothetical protein FLJ39502 FLJ39963 20.67 Hs.512228 349075 AK097282 hypothetical protein FLJ39963 FLJ90650 5.67 Hs.98288 206338 AI246369 laeverin FLJ90661 5.71 Hs.256632 146547 NM_173502 hypothetical protein FLJ90661 FMN2 25.08 Hs.24889 56776 606373 BC014364 formin 2 FMO5 6.81 Hs.396595 2330 603957 NM_001461 flavin containing monooxygenase 5 FNBP2 7.60 Hs.5003 23380 606524 AI263819 formin binding protein 2 FOXA1 8.62 Hs.163484 3169 602294 NM_004496 forkhead box A1 FOXA2 252.32 Hs.155651 3170 600288 AB028021 forkhead box A2 FOXC1 9.62 Hs.348883 2296 601090 NM_001453 forkhead box C1 FOXI1 25.76 Hs.87236 2299 601093 NM_012188 forkhead box I1 FOXQ1 43.02 Hs.297452 94234 AI676059 forkhead box Q1 FUBP3 5.53 Hs.98751 8939 603536 AW085489 far upstream element (FUSE) binding protein 3 FZD5 10.18 Hs.152251 7855 601723 NM_003468 frizzled homolog 5 (Drosophila) FZD8 37.68 Hs.302634 8325 606146 AL121749 frizzled homolog 8 (Drosophila) GAL3ST1 7.31 Hs.17958 9514 602300 NM_004861 galactose-3-O-sulfotransferase 1 GATA3 13.22 Hs.169946 2625 131320 AI796169 GATA binding protein 3 GATA4 44.12 Hs.243987 2626 600576 AV700724 GATA binding protein 4 GATA6 24.26 Hs.50924 2627 601656 D87811 GATA binding protein 6 GATM 5.63 Hs.75335 2628 602360 NM_001482 glycine amidinotransferase (L-arginine:glycine amidinotransferase) GBA 5.30 Hs.282997 2629 606463 D13287 glucosidase, beta; acid (includes glucosylceramidase) GDF15 5.06 Hs.296638 9518 605312 AA129612 growth differentiation factor 15 GJA4 13.38 Hs.296310 2701 121012 NM_002060 gap junction protein, alpha 4, 37 kDa (connexin 37) GJB3 7.07 Hs.415770 2707 603324 BF060667 gap junction protein, beta 3, 31 kDa (connexin 31) GMPR 5.80 Hs.1435 2766 139265 NM_006877 guanosine monophosphate reductase GNG2 9.92 Hs.112928 54331 606981 AK026424 guanine nucleotide binding protein (G protein), gamma 2 GPC6 6.51 Hs.508411 10082 604404 AI651255 glypican 6 GPM6A 15.76 Hs.75819 2823 601275 D49958 glycoprotein M6A GPR115 6.03 Hs.150131 221393 W67511 G protein-coupled receptor 115 GPR126 8.44 Hs.419170 57211 AL033377 G protein-coupled receptor 126 GPR2 7.86 Hs.278446 2826 600240 NM_016602 G protein-coupled receptor 2 GPR37 33.44 Hs.406094 2861 602583 U87460 G protein-coupled receptor 37 (endothelin receptor type B-like) GPR39 15.38 Hs.512073 2863 602886 AV717094 G protein-coupled receptor 39 GPR49 21.48 Hs.166705 8549 606667 AL524520 G protein-coupled receptor 49 GPR81 6.22 Hs.326712 27198 606923 AF345568 G protein-coupled receptor 81 GPSM2 16.16 Hs.278338 29899 NM_013296 G-protein signalling modulator 2 (AGS3-like, C. elegans) GREB1 5.95 Hs.438037 9687 NM_014668 GREB1 protein GRK7 5.60 Hs.351818 131890 606987 NM_139209 G protein-coupled receptor kinase 7 GRP 19.11 Hs.153444 2922 137260 NM_002091 gastrin-releasing peptide GSC 524.27 Hs.440438 145258 138890 AY177407 goosecoid GW112 11.00 Hs.273321 10562 AL390736 differentially expressed in hematopoietic lineages H2AFY 29.04 Hs.75258 9555 AF044286 H2A histone family, member Y HAS2 7.56 Hs.159226 3037 601636 AI374739 hyaluronan synthase 2 HCN1 14.55 Hs.353176 348980 602780 BM682352 hyperpolarization activated cyclic nucleotide-gated potassium channel 1 Hes4 6.20 Hs.154029 57801 608060 NM_021170 bHLH factor Hes4 HGF 5.02 Hs.396530 3082 142409 U46010 hepatocyte growth factor (hepapoietin A; scatter factor) HHEX 6.58 Hs.118651 3087 604420 Z21533 hematopoietically expressed homeobox HIPK2 20.25 Hs.397465 28996 606868 AF207702 homeodomain interacting protein kinase 2 HLXB9 18.27 Hs.37035 3110 142994 AI738662 homeo box HB9 HNF4A 38.25 Hs.54424 3172 600281 AI032108 hepatocyte nuclear factor 4, alpha HOXD13 15.68 Hs.152414 3239 142989 NM_000523 homeo box D13 HP 14.05 Hs.403931 3240 140100 NM_005143 haptoglobin HSD17B1 6.50 Hs.448861 3292 109684 NM_000413 hydroxysteroid (17-beta) dehydrogenase 1 HTATIP2 5.54 Hs.90753 10553 605628 BG153401 HIV-1 Tat interactive protein 2, 30 kDa ICOSL 5.24 Hs.14155 23308 605717 AL355690 inducible T-cell co-stimulator ligand IFIT5 6.36 Hs.252839 24138 NM_012420 interferon-induced protein with tetratricopeptide repeats 5 IGFBP6 20.26 Hs.274313 3489 146735 NM_002178 insulin-like growth factor binding protein 6 IHH 5.76 Hs.115274 3549 600726 AA628967 Indian hedgehog homolog (Drosophila) IL18R1 25.01 Hs.159301 8809 604494 NM_003855 interleukin 18 receptor 1 IL1R1 5.36 Hs.82112 3554 147810 NM_000877 interleukin 1 receptor, type I IMAP1 47.52 Hs.159955 170575 608084 BC029442 immunity associated protein 1 ITGA1 6.58 Hs.439320 3672 192968 BG619261 integrin, alpha 1 ITGA5 5.66 Hs.149609 3678 135620 NM_002205 integrin, alpha 5 (fibronectin receptor, alpha polypeptide) ITGA9 13.12 Hs.222 3680 603963 AI479176 integrin, alpha 9 ITPKB 19.74 Hs.78877 3707 147522 AA348410 inositol 1,4,5-trisphosphate 3-kinase B JMJD3 12.61 Hs.103915 23135 AI830331 jumonji domain containing 3 KCNG1 12.30 Hs.118695 3755 603788 AI332979 potassium voltage-gated channel, subfamily G, member 1 KCNH8 13.59 Hs.410629 131096 NM_144633 potassium voltage-gated channel, subfamily H (eag-related), member 8 KCNJ3 22.66 Hs.199776 3760 601534 AK026384 potassium inwardly-rectifying channel, subfamily J, member 3 KCNK1 6.73 Hs.376874 3775 601745 AL833343 potassium channel, subfamily K, member 1 KCNK12 7.71 Hs.252617 56660 607366 NM_022055 potassium channel, subfamily K, member 12 KCNV2 26.04 Hs.441357 169522 607604 AI206888 potassium channel, subfamily V, member 2 KIAA0258 6.12 Hs.47313 9827 AI690081 KIAA0258 KIAA0318 5.49 Hs.225014 23504 BE549770 RIM binding protein 2 KIAA0484 5.10 57240 AA732995 KIAA0484 protein KIAA0626 5.02 Hs.178121 9848 NM_021647 KIAA0626 gene product KIAA0774 7.72 Hs.22201 23281 AI818409 KIAA0774 KIAA0792 5.85 Hs.119387 9725 AW510783 KIAA0792 gene product KIAA0825 5.03 Hs.194755 23004 AB020632 KIAA0825 protein KIAA0882 23.04 Hs.411317 23158 AI348094 KIAA0882 protein KIAA0895 12.12 Hs.6224 23366 AB020702 KIAA0895 protein KIAA1161 11.92 Hs.181679 57462 AB032987 KIAA1161 KIAA1202 22.67 Hs.380697 57477 AI005420 KIAA1202 protein KIAA1211 5.43 Hs.205293 57482 AI991996 KIAA1211 protein KIAA1447 5.19 Hs.512733 57597 NM_024696 KIAA1447 protein KIAA1618 5.21 Hs.437033 57714 AA976354 KIAA1618 KIAA1679 5.98 Hs.68533 80731 AB051466 KIAA1679 protein KIAA1728 7.82 Hs.437362 85461 AB051515 KIAA1728 protein KIAA1729 5.19 Hs.99073 85460 AI138969 KIAA1729 protein KIAA1856 7.82 Hs.383245 84629 AI936523 KIAA1856 protein KIFC3 17.78 Hs.23131 3801 604535 BC001211 kinesin family member C3 KLF5 5.42 Hs.84728 688 602903 AF132818 Kruppel-like factor 5 (intestinal) KYNU 12.90 Hs.444471 8942 236800 D55639 kynureninase (L-kynurenine hydrolase) LAMB3 6.26 Hs.436983 3914 150310 L25541 laminin, beta 3 LAMP3 6.00 Hs.10887 27074 605883 NM_014398 lysosomal-associated membrane protein 3 LEFTB 10.76 Hs.278239 10637 603037 NM_020997 left-right determination, factor B LEPREL1 5.44 Hs.42824 55214 NM_018192 leprecan-like 1 LHX1 13.00 Hs.443727 3975 601999 NM_005568 LIM homeobox 1 LIFR 10.18 Hs.446501 3977 151443 AA701657 leukemia inhibitory factor receptor LMLN 7.70 Hs.432613 89782 BF056991 leishmanolysin-like (metallopeptidase M8 family) LOC128153 7.17 Hs.99214 128153 AA905508 hypothetical protein BC014608 LOC131873 10.87 Hs.263560 131873 AI761416 hypothetical protein LOC131873 LOC132604 6.82 132604 BC044793 GalNAc transferase 10 isoform-like LOC148898 5.54 Hs.61884 148898 AW298597 hypothetical protein BC007899 LOC148987 7.40 148987 BC040313 hypothetical protein LOC148987 LOC149414 11.75 149414 AF218941 formin 2-Like LOC151878 7.05 151878 AW009761 hypothetical protein LOC151878 LOC152084 5.62 152084 BC041967 hypothetical protein LOC152084 LOC153682 25.68 153682 AL137383 hypothetical protein LOC153682 LOC157278 21.30 Hs.363026 157278 AK074886 hypothetical protein LOC157278 LOC162073 5.32 Hs.28890 162073 BC015343 hypothetical protein LOC162073 LOC199920 12.19 199920 AI452457 hypothetical protein LOC199920 LOC201175 8.06 Hs.205326 201175 AF258593 hypothetical protein LOC201175 LOC203806 5.74 Hs.256916 203806 AK092565 hypothetical protein LOC203806 LOC253012 7.75 Hs.443169 253012 AA600175 hypothetical protein LOC253012 LOC253970 5.72 253970 BE218152 hypothetical protein LOC253970 LOC283537 68.29 Hs.117167 283537 AK026720 hypothetical protein LOC283537 LOC283666 6.05 283666 AW006185 hypothetical protein LOC283666 LOC283887 5.17 Hs.171285 283887 AI215529 hypothetical protein LOC283887 LOC284001 6.04 Hs.526416 284001 AF007146 hypothetical protein LOC284001 LOC284367 14.25 Hs.132045 284367 AI801574 hypothetical protein LOC284367 LOC284542 14.80 Hs.61504 284542 BF060736 hypothetical protein LOC284542 LOC284561 6.01 284561 AK023548 hypothetical protein LOC284561 LOC284615 8.69 284615 AL359622 hypothetical protein LOC284615 LOC284739 5.97 Hs.97840 284739 AL157500 hypothetical protein LOC284739 LOC284898 5.82 Hs.350813 284898 BC036876 hypothetical protein LOC284898 LOC284950 6.21 284950 AK095038 hypothetical protein LOC284950 LOC285045 5.97 Hs.434660 285045 AK095182 hypothetical protein LOC285045 LOC285878 5.63 285878 AI420977 hypothetical protein LOC285878 LOC339005 5.02 Hs.212670 339005 AI824078 hypothetical protein LOC339005 LOC348094 12.72 Hs.207157 348094 AI760630 hypothetical protein LOC348094 LOC349136 7.15 Hs.174373 349136 AI968904 hypothetical protein LOC349136 LOC360030 6.38 Hs.385546 360030 BC036226 homeobox C14 LOC375616 25.34 Hs.443744 375616 AI955614 kielin-like LOC51066 21.78 Hs.113019 51066 NM_015931 fls485 LOC51326 5.04 Hs.416744 51326 AF493886 ARF protein LOC90342 6.85 90342 AL133022 similar to fer-1 like protein 3 LOC90736 9.70 Hs.415414 90736 BG285399 hypothetical protein BC000919 LOC91526 7.85 Hs.11571 91526 AU157224 hypothetical protein DKFZp434D2328 LRIG3 26.20 Hs.19669 121227 AI627704 leucine-rich repeats and immunoglobulin-like domains 3 LRRFIP1 5.61 Hs.512387 9208 603256 BC004958 leucine rich repeat (in FLII) interacting protein 1 LW-1 32.53 51402 NM_016153 LW-1 MADH6 6.35 Hs.153863 4091 602931 AI193899 MAD, mothers against decapentaplegic homolog 6 (Drosophila) MAML3 8.03 Hs.310320 55534 AI569476 mastermind-like 3 (Drosophila) MAN1A1 10.19 Hs.255149 4121 604344 BG287153 mannosidase, alpha, class 1A, member 1 MANEA 18.25 Hs.46903 79694 AI587307 mannosidase, endo-alpha MAP3K13 10.61 Hs.406946 9175 604915 NM_004721 mitogen-activated protein kinase kinase kinase 13 MAP3K4 6.15 Hs.390428 4216 602425 AI633559 mitogen-activated protein kinase kinase kinase 4 MATN3 10.63 Hs.278461 4148 602109 NM_002381 matrilin 3 MCC 9.39 Hs.409515 4163 159350 BE967311 mutated in colorectal cancers MCLC 13.56 Hs.93121 23155 AA406603 Mid-1-related chloride channel 1 MERTK 6.55 Hs.306178 10461 604705 NM_006343 c-mer proto-oncogene tyrosine kinase MGC13057 9.53 Hs.389311 84281 BC005083 hypothetical protein MGC13057 MGC14276 6.08 Hs.434283 253150 BE195670 hypothetical protein MGC14276 MGC14289 5.00 Hs.152618 92092 AI188445 similar to RIKEN cDNA 1200014N16 gene MGC19764 6.65 Hs.14691 162394 AI435399 hypothetical protein MGC19764 MGC26989 6.83 Hs.430223 254268 AL832216 hypothetical protein MGC26989 MGC33835 10.65 Hs.367947 222662 BC028630 hypothetical protein MGC33835 MGC34032 16.41 Hs.213897 204962 AA001450 hypothetical protein MGC34032 MGC35130 10.58 Hs.388746 148581 NM_152489 hypothetical protein MGC35130 MGC35402 6.35 Hs.146844 399669 AK096828 hypothetical protein MGC35402 MGC39518 5.83 Hs.372046 285172 BC039295 hypothetical protein MGC39518 MGC39821 11.27 Hs.351906 284440 BI599587 hypothetical protein MGC39821 MGC39900 8.56 Hs.422848 286527 H09657 hypothetical protein MGC39900 MGC45441 9.54 Hs.36567 149473 AU153816 hypothetical protein MGC45441 MGC45594 8.34 Hs.408128 284273 BC033780 hypothetical protein MGC45594 MGC46719 8.84 Hs.356109 128077 AW500180 hypothetical protein MGC46719 MGC52498 8.36 Hs.424589 348378 AI202632 hypothetical protein MGC52498 MGC5395 10.77 Hs.378738 79026 BG287862 hypothetical protein MGC5395 MGC8721 5.00 Hs.279921 51669 AI351653 hypothetical protein MGC8721 MGST2 13.23 Hs.81874 4258 601733 NM_002413 microsomal glutathione S-transferase 2 MIB 5.49 Hs.34892 57534 608677 BE048628 DAPK-interacting protein 1 MIDORI 12.95 Hs.301242 57538 AB037751 likely ortholog of mouse myocytic induction/ differentiation originator MIXL1 16.37 Hs.282079 83881 AF211891 Mix1 homeobox-like 1 (Xenopus laevis) MME 12.25 Hs.307734 4311 120520 NM_007287 membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10) MMP14 13.59 Hs.2399 4323 600754 NM_004995 matrix metalloproteinase 14 (membrane-inserted) MMP21 6.36 Hs.314141 118856 608416 NM_147191 matrix metalloproteinase 21 MPRG 12.47 Hs.257511 54852 607781 AI934557 membrane progestin receptor gamma MRC1 5.02 Hs.75182 4360 153618 NM_002438 mannose receptor, C type 1 MSMB 25.23 Hs.255462 4477 157145 NM_002443 microseminoprotein, beta- MTUS1 6.10 Hs.7946 57509 AL096842 mitochondrial tumor suppressor 1 MYBPC1 7.33 Hs.169849 4604 160794 BF593509 myosin binding protein C, slow type MYCT1 14.81 Hs.18160 80177 AI242583 myc target 1 MYL4 11.75 Hs.356717 4635 160770 X58851 myosin, light polypeptide 4, alkali; atrial, embryonic MYL7 38.38 Hs.75636 58498 NM_021223 myosin, light polypeptide 7, regulatory MYO3A 6.69 Hs.148228 53904 606808 AA443280 myosin IIIA MYOCD 6.86 Hs.42128 93649 606127 AI093327 myocardin NBL1 8.62 Hs.439671 4681 600613 NM_005380 neuroblastoma, suppression of tumorigenicity 1 NBR2 6.10 Hs.500268 10230 NM_005821 neighbor of BRCA1 gene 2 NCR1 9.38 Hs.97084 9437 604530 NM_004829 natural cytotoxicity triggering receptor 1 NEBL 10.59 Hs.5025 10529 605491 BE502910 nebulette NEXN 9.60 Hs.22370 91624 AF114264 nexilin (F actin binding protein) NFASC 35.64 Hs.13349 23114 AI821777 neurofascin NFATC2 6.56 Hs.356321 4773 600490 AI770171 nuclear factor of activated T-cells, cytoplasmic, calcineurin- dependent 2 NFKBIA 6.83 Hs.81328 4792 164008 AI078167 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha NFKBIL1 6.39 Hs.2764 4795 601022 AF097419 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1 NODAL 7.89 Hs.370414 4838 601265 AI050866 nodal homolog (mouse) NOG 6.96 Hs.248201 9241 602991 AL575177 noggin NOL3 5.46 Hs.462911 8996 605235 AF043244 nucleolar protein 3 (apoptosis repressor with CARD domain) NPL 6.11 Hs.64896 80896 AI368358 N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) NPPB 35.43 Hs.219140 4879 600295 NM_002521 natriuretic peptide precursor B NR0B1 19.33 Hs.268490 190 300473 NM_000475 nuclear receptor subfamily 0, group B, member 1 NR3C1 6.71 Hs.126608 2908 138040 AI934556 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) NRG1 15.88 Hs.453951 3084 142445 NM_013959 neuregulin 1 NRP1 14.29 Hs.173548 8829 602069 AF145712 neuropilin 1 NRTN 5.20 Hs.234775 4902 602018 AL161995 neurturin NTN4 57.13 Hs.102541 59277 AF278532 netrin 4 NUDT14 7.42 Hs.436170 256281 AF111170 nudix (nucleoside diphosphate linked moiety X)-type motif 14 NUDT4 13.66 Hs.355399 11163 AW511135 nudix (nucleoside diphosphate linked moiety X)-type motif 4 OMD 6.06 Hs.94070 4958 NM_005014 osteomodulin OR2A4 5.43 Hs.444988 79541 AC005587 olfactory receptor, family 2, subfamily A, member 4 OR51B2 5.59 79345 AF137396 olfactory receptor, family 51, subfamily B, member 2 OSTF1 5.20 Hs.47011 26578 BU929456 osteoclast stimulating factor 1 P101-PI3K 5.44 Hs.278901 23533 BG236366 phosphoinositide-3-kinase, regulatory subunit, polypeptide p101 P2RY12 9.81 Hs.444983 64805 600515 AA810452 purinergic receptor P2Y, G-protein coupled, 12 PAG 18.02 Hs.266175 55824 605767 AK000680 phosphoprotein associated with glycosphingolipid-enriched microdomains PAX6 48.76 Hs.89506 5080 607108 AW088232 paired box gene 6 (aniridia, keratitis) PCDH10 12.50 Hs.146858 57575 608286 AI640307 protocadherin 10 PCDH7 6.54 Hs.443020 5099 602988 BE644809 BH-protocadherin (brain-heart) PCDHA2 6.83 56146 606308 BC003126 protocadherin alpha 2 PCDHB13 6.32 Hs.283803 56123 606339 AA489646 protocadherin beta 13 PCDHB5 10.65 Hs.119693 26167 606331 AF152528 protocadherin beta 5 PCTP 6.11 Hs.285218 58488 606055 NM_021213 phosphatidylcholine transfer protein PDE4D 8.34 Hs.28482 5144 600129 U50157 phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) PDE4DIP 7.74 Hs.502577 9659 608117 H24473 phosphodiesterase 4D interacting protein (myomegalin) PDE4DIP 6.27 Hs.502582 9659 608117 AB007923 phosphodiesterase 4D interacting protein (myomegalin) PDZK1 29.68 Hs.15456 5174 603831 NM_002614 PDZ domain containing 1 PHLDB2 5.43 Hs.7378 90102 AK025444 pleckstrin homology-like domain, family B, member 2 PIGC 5.04 Hs.386487 5279 601730 AL035301 phosphatidylinositol glycan, class C PITX2 12.09 Hs.92282 5308 601542 NM_000325 paired-like homeodomain transcription factor 2 PKHD1L1 11.52 Hs.170128 93035 607843 AV706971 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 PLA1A 6.48 Hs.17752 51365 607460 NM_015900 phospholipase A1 member A PLA2G4D 5.98 Hs.380225 283748 BC034571 phospholipase A2, group IVD (cytosolic) PLAGL1 6.84 Hs.132911 5325 603044 NM_002656 pleiomorphic adenoma gene-like 1 PLCE1 18.17 Hs.103417 51196 608414 NM_016341 phospholipase C, epsilon 1 PLD1 11.78 Hs.380819 5337 602382 AI378587 phospholipase D1, phophatidylcholine-specific PLXNA2 23.20 Hs.300622 5362 601054 AI688418 plexin A2 PLXNA2 5.48 Hs.350065 5362 601054 AI694545 plexin A2 PORCN 6.62 Hs.386453 64840 NM_022825 porcupine homolog (Drosophila) PPAPDC1 7.83 Hs.40479 196051 BF130943 phosphatidic acid phosphatase type 2 domain containing 1 PPFIBP2 17.00 Hs.12953 8495 603142 AI692180 PTPRF interacting protein, binding protein 2 (liprin beta 2) PPP1R16B 8.46 Hs.45719 26051 AB020630 protein phosphatase 1, regulatory (inhibitor) subunit 16B PPP3CC 10.69 Hs.75206 5533 114107 NM_005605 protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma) PRDM1 13.93 Hs.381140 639 603423 AI692659 PR domain containing 1, with ZNF domain PREX1 6.21 Hs.437257 57580 606905 AL445192 phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1 PRND 12.95 Hs.406696 23627 604263 AL133396 prion protein 2 (dublet) PRO0471 5.73 Hs.381337 28994 AF111846 PRO0471 protein PRO2012 8.53 Hs.283066 55478 NM_018614 hypothetical protein PRO2012 PROS1 13.38 Hs.64016 5627 176880 NM_000313 protein S (alpha) PRSS2 205.03 Hs.435699 5646 NM_002770 protease, serine, 3 (mesotrypsin) PRV1 24.58 Hs.232165 57126 162860 NM_020406 polycythemia rubra vera 1 PTGFR 16.53 Hs.89418 5737 600563 NM_000959 prostaglandin F receptor (FP) PTPN5 6.24 Hs.79092 84867 176879 H29627 protein tyrosine phosphatase, non-receptor type 5 (striatum- enriched) PTPRM 18.83 Hs.154151 5797 176888 BC029442 protein tyrosine phosphatase, receptor type, M QPCT 8.60 Hs.79033 25797 607065 NM_012413 glutaminyl-peptide cyclotransferase (glutaminyl cyclase) RAB17 20.30 Hs.44278 64284 NM_022449 RAB17, member RAS oncogene family RAB18 5.00 Hs.414357 22931 602207 AW367507 RAB18, member RAS oncogene family RAI1 7.07 Hs.438904 10743 607642 BF984830 retinoic acid induced 1 RARB 5.89 Hs.436538 5915 180220 NM_000965 retinoic acid receptor, beta RASGEF1B 6.86 Hs.352552 153020 BC036784 RasGEF domain family, member 1B RASGRP1 7.86 Hs.189527 10125 603962 NM_005739 RAS guanyl releasing protein 1 (calcium and DAG-regulated) RASSF6 5.44 Hs.158857 166824 AI167789 Ras association (RalGDS/AF-6) domain family 6 RBM20 11.00 Hs.116630 282996 AI539118 RNA binding motif protein 20 RBM24 21.38 Hs.201619 221662 AI677701 RNA binding motif protein 24 RBP5 14.34 Hs.246046 83758 AY007436 retinol binding protein 5, cellular RBPMS 5.21 Hs.195825 11030 601558 AI017095 RNA binding protein with multiple splicing RGC32 27.89 Hs.76640 28984 NM_014059 response gene to complement 32 RGS11 7.12 Hs.65756 8786 603895 NM_003834 regulator of G-protein signalling 11 RGS13 5.15 Hs.17165 6003 607190 BC036950 regulator of G-protein signalling 13 RGS5 5.70 Hs.24950 8490 603276 AF159570 regulator of G-protein signalling 5 RGS8 7.50 Hs.458417 85397 607189 R37101 regulator of G-protein signalling 8 RHOBTB3 21.23 Hs.31653 22836 607353 NM_014899 Rho-related BTB domain containing 3 RIN2 7.00 Hs.446304 54453 AL136924 Ras and Rab interactor 2 RNASE1 8.63 Hs.78224 6035 180440 NM_002933 ribonuclease, RNase A family, 1 (pancreatic) RNASE4 10.29 Hs.283749 6038 601030 AI761728 ribonuclease, RNase A family, 4 ROR2 10.29 Hs.208080 4920 602337 NM_004560 receptor tyrosine kinase-like orphan receptor 2 RP26 8.04 Hs.145140 375298 608381 AI936034 retinitis pigmentosa 26 (autosomal recessive) RS1 5.49 Hs.149376 6247 312700 AL049684 retinoschisis (X-linked, juvenile) 1 RTN4RL1 60.66 Hs.22917 146760 H06251 reticulon 4 receptor-like 1 RUFY2 5.60 Hs.297044 55680 NM_017987 RUN and FYVE domain containing 2 RWDD3 9.89 Hs.196585 25950 AW295367 RWD domain containing 3 S100A10 6.73 Hs.143873 6281 114085 BF126155 S100 calcium binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11)) S100A11 7.07 Hs.417004 6282 603114 NM_005620 S100 calcium binding protein A11 (calgizzarin) S100A13 7.21 Hs.446592 6284 601989 NM_005979 S100 calcium binding protein A13 S100A14 26.13 Hs.288998 57402 607986 NM_020672 S100 calcium binding protein A14 S100A16 11.27 Hs.8182 140576 AA045184 S100 calcium binding protein A16 S100A2 5.97 Hs.515713 6273 176993 NM_005978 S100 calcium binding protein A2 S100Z 12.38 Hs.352172 170591 AF437876 S100Z protein SAMD3 12.06 Hs.440508 154075 AI129628 sterile alpha motif domain containing 3 SCA1 8.18 Hs.434961 6310 601556 BF438383 spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1) SCD4 6.62 Hs.379191 79966 608370 AL571375 stearoyl-CoA desaturase 4 SCN11A 5.98 Hs.186877 11280 604385 AF150882 sodium channel, voltage-gated, type XI, alpha SEC15L1 8.34 Hs.272374 54536 AF220217 SEC15-like 1 (S. cerevisiae) SEMA3A 7.44 Hs.252451 10371 603961 BF102683 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A SEMA3E 135.96 Hs.528721 9723 NM_012431 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E SEMA5A 5.42 Hs.528707 9037 NM_003966 sema domain, seven thrombospondin repeats (type 1 and type 1- like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A SERHL 27.81 Hs.398085 94009 607979 AL450314 serine hydrolase-like SET7 5.97 Hs.160208 80854 606594 AK024846 SET domain-containing protein 7 SGPP1 5.85 Hs.24678 81537 BE880703 sphingosine-1-phosphate phosphatase 1 SGSH 10.71 Hs.31074 6448 605270 NM_000199 N-sulfoglucosamine sulfohydrolase (sulfamidase) SH3BGR 8.65 Hs.47438 6450 602230 NM_007341 SH3 domain binding glutamic acid-rich protein SHOX2 12.75 Hs.55967 6474 602504 AF022654 short stature homeobox 2 SHREW1 15.74 Hs.25924 55966 AA835004 transmembrane protein SHREW1 SIAT7B 13.12 Hs.288215 10610 NM_006456 sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3- beta-galactosyl-1,3)-N-acetyl galactosaminide alpha- 2,6-sialyltransferase) B. SIAT8A 34.34 Hs.408614 6489 601123 L32867 sialyltransferase 8A (alpha-N-acetylneuraminate: alpha-2,8- sialyltransferase, GD3 synthase) SIAT8B 7.63 Hs.302341 8128 602546 NM_006011 sialyltransferase 8B (alpha-2,8-sialyltransferase) SIAT8C 6.55 Hs.298923 51046 NM_015879 sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8- sialyltransferase) SIAT8D 161.93 Hs.308628 7903 602547 AI422986 sialyltransferase 8D (alpha-2,8-polysialyltransferase) SIAT9 13.35 Hs.415117 8869 604402 AI017540 sialyltransferase 9 (CMP-NeuAc:lactosylceramide alpha-2,3- sialyltransferase; GM3 synthase) SIGLEC10 7.88 Hs.284813 89790 606091 NM_033130 sialic acid binding Ig-like lectin 10 SIPA1L2 5.51 Hs.406879 57568 AB037810 signal-induced proliferation-associated 1 like 2 SLAC2-B 5.01 Hs.138380 23086 AB014524 SLAC2-B SLC1A1 14.09 Hs.91139 6505 133550 AW235061 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 SLC1A7 5.45 Hs.104637 6512 604471 NM_006671 solute carrier family 1 (glutamate transporter), member 7 SLC26A7 18.00 Hs.354013 115111 608479 AI758950 solute carrier family 26, member 7 SLC34A2 7.97 Hs.441716 10568 604217 AF146796 solute carrier family 34 (sodium phosphate), member 2 SLC35A3 7.42 Hs.448979 23443 605632 BC005136 solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 SLC35F3 11.46 Hs.158748 148641 BF968270 solute carrier family 35, member F3 SLC40A1 44.06 Hs.409875 30061 604653 AL136944 solute carrier family 40 (iron-regulated transporter), member 1 SLC5A9 79.96 Hs.37890 200010 AI767388 solute carrier family 5 (sodium/glucose cotransporter), member 9 SLC6A20 6.86 Hs.413095 54716 605616 NM_020208 solute carrier family 6 (neurotransmitter transporter), member 20 SLCO2A1 12.84 Hs.83974 6578 601460 NM_005630 solute carrier organic anion transporter family, member 2A1 SLITRK2 13.29 Hs.320368 84631 AL109653 SLIT and NTRK-like family, member 2 SMARCD3 7.37 Hs.444445 6604 601737 NM_003078 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 SMPD1 5.76 Hs.77813 6609 607608 M59917 sphingomyelin phosphodiesterase 1, acid lysosomal (acid sphingomyelinase) SOCS1 5.92 Hs.50640 8651 603597 U88326 suppressor of cytokine signaling 1 SOCS3 9.41 Hs.436943 9021 604176 AI244908 suppressor of cytokine signaling 3 SORCS1 24.07 Hs.348923 114815 606283 AI675836 sortilin-related VPS10 domain containing receptor 1 SOX17 30.20 Hs.98367 64321 NM_022454 SRY (sex determining region Y)-box 17 SOX18 10.36 Hs.8619 54345 601618 NM_018419 SRY (sex determining region Y)-box 18 SPOCK3 62.58 Hs.159425 50859 607989 AI808090 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3 SPTAN1 5.56 Hs.387905 6709 182810 AK026484 spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) SRGAP1 9.61 Hs.408259 57522 606523 BC029919 SLIT-ROBO Rho GTPase activating protein 1 SSX2 11.44 Hs.289105 6757 300192 BC002818 synovial sarcoma, X breakpoint 2 SSX3 12.43 Hs.178749 10214 300325 NM_021014 synovial sarcoma, X breakpoint 3 SSX4 8.27 Hs.278632 6759 300326 BC005325 synovial sarcoma, X breakpoint 4 STAT4 6.73 Hs.80642 6775 600558 NM_003151 signal transducer and activator of transcription 4 STC1 18.86 Hs.25590 6781 601185 U46768 stanniocalcin 1 STMN2 33.93 Hs.90005 11075 600621 BF967657 stathmin-like 2 SULF2 5.84 Hs.43857 55959 AL133001 sulfatase 2 SULT1E1 5.08 Hs.54576 6783 600043 NM_005420 sulfotransferase family 1E, estrogen-preferring, member 1 SV2B 16.36 Hs.8071 9899 185861 NM_014848 synaptic vesicle glycoprotein 2B SYNE1 8.40 Hs.282117 23345 608441 AF043290 spectrin repeat containing, nuclear envelope 1 TAF11 5.01 Hs.83126 6882 600772 BQ709323 TAF11 RNA polymerase II, TATA box binding protein (TBP)- associated factor, 28 kDa TAGLN2 9.05 Hs.406504 8407 604634 NM_003564 transgelin 2 TAIP-2 9.08 Hs.287442 80034 NM_024969 TGF-beta induced apotosis protein 2 TAL2 6.00 Hs.247978 6887 186855 NM_005421 T-cell acute lymphocytic leukemia 2 TA-LRRP 7.71 Hs.387915 23507 R41498 T-cell activation leucine repeat-rich protein TCF2 9.87 Hs.408093 6928 189907 NM_000458 transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor TDRD7 19.46 Hs.416543 23424 AW129593 tudor domain containing 7 TGFB1 5.40 Hs.1103 7040 190180 BC000125 transforming growth factor, beta 1 (Camurati-Engelmann disease) TIMP3 5.72 Hs.245188 7078 188826 NM_000362 tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory) TIRP 6.36 Hs.278391 353376 608321 AI400110 TRIF-related adaptor molecule TLE2 8.87 Hs.332173 7089 601041 M99436 transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila) TM4SF1 8.02 Hs.351316 4071 191155 AI189753 transmembrane 4 superfamily member 1 TM4SF12 5.88 Hs.16529 23554 NM_012338 transmembrane 4 superfamily member 12 TMOD1 74.09 Hs.374849 7111 190930 NM_003275 tropomodulin 1 TNFSF10 15.05 Hs.387871 8743 603598 NM_003810 tumor necrosis factor (ligand) superfamily, member 10 TNNC1 31.06 Hs.118845 7134 191040 AF020769 troponin C, slow TPK1 5.18 Hs.127548 27010 606370 NM_022445 thiamin pyrophosphokinase 1 TPTE 11.46 Hs.122986 7179 604336 AL137389 transmembrane phosphatase with tensin homology TRADD 8.22 Hs.89862 8717 603500 NM_003789 TNFRSF1A-associated via death domain TRDN 12.67 Hs.159090 10345 603283 AA192306 triadin TRPA1 103.37 Hs.137674 8989 604775 AA502609 transient receptor potential cation channel, subfamily A, member 1 TRPM4 5.00 Hs.31608 54795 606936 NM_017636 transient receptor potential cation channel, subfamily M, member 4 TSGA10 6.41 Hs.416032 80705 607166 AY014284 testis specific, 10 TSHR 5.96 Hs.123078 7253 603372 BE045816 thyroid stimulating hormone receptor TSPYL5 17.94 Hs.173094 85453 AI096375 TSPY-like 5 TTC3 12.26 Hs.132605 7267 602259 AI652848 tetratricopeptide repeat domain 3 TTLL3 7.35 Hs.511982 26140 AA534291 tubulin tyrosine ligase-like family, member 3 TTN 76.16 Hs.434384 7273 188840 NM_003319 titin TUBE1 8.85 Hs.34851 51175 607345 BE550254 tubulin, epsilon 1 UBE2J1 7.26 Hs.184325 51465 N64079 ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast) UBXD3 5.81 Hs.432503 127733 T86344 UBX domain containing 3 UNC13C 32.43 Hs.112921 145790 AL834407 unc-13 homolog C (C. elegans) UNC93A 32.18 Hs.267749 54346 607995 AL021331 unc-93 homolog A (C. elegans) UNQ467 5.30 Hs.112457 388533 W69083 KIPV467 UNQ827 5.08 Hs.516819 400830 BE044548 KFLL827 USP3 7.90 Hs.251636 9960 604728 AF077040 ubiquitin specific protease 3 USP53 6.36 Hs.135457 54532 AW188464 ubiquitin specific protease 53 VANGL1 7.57 Hs.99598 81839 NM_024062 vang-like 1 (van gogh, Drosophila) VCAM1 18.40 Hs.109225 7412 192225 NM_001078 vascular cell adhesion molecule 1 VGCNL1 5.61 Hs.391323 259232 BE220480 voltage gated channel like 1 VIL1 14.42 Hs.512713 7429 193040 NM_007127 villin 1 VNN3 6.94 Hs.183656 55350 606592 NM_078625 vanin 3 VPS13C 6.16 Hs.328109 54832 AA828371 vacuolar protein sorting 13C (yeast) VTN 6.33 Hs.2257 7448 193190 NM_000638 vitronectin (serum spreading factor, somatomedin B, complement S-protein) VWF 13.24 Hs.440848 7450 193400 NM_000552 von Willebrand factor WASPIP 5.76 Hs.401414 7456 602357 AW058622 Wiskott-Aldrich syndrome protein interacting protein WBSCR24 6.28 Hs.126451 155382 AI521163 Williams Beuren syndrome chromosome region 24 WDR31 6.10 Hs.133331 114987 BF589326 WD repeat domain 31 WFDC2 8.49 Hs.2719 10406 NM_006103 WAP four-disulfide core domain 2 WT1 19.92 Hs.1145 7490 607102 NM_024426 Wilms tumor 1 XIST 5.11 7503 314670 BE644917 X (inactive)-specific transcript XLHSRF-1 10.49 Hs.9740 25981 AI004779 heat shock regulated 1 YAF2 12.36 Hs.348380 10138 607534 R56794 YY1 associated factor 2 YPEL2 15.77 Hs.368672 388403 BE502982 yippee-like 2 (Drosophila) ZAP70 14.98 Hs.234569 7535 176947 AB083211 zeta-chain (TCR) associated protein kinase 70 kDa ZFPM2 6.50 Hs.106309 23414 603693 NM_012082 zinc finger protein, multitype 2 ZNF148 5.13 Hs.442787 7707 601897 AW594167 zinc finger protein 148 (pHZ-52) ZNF335 7.13 Hs.174193 63925 NM_022095 zinc finger protein 335 ZNF396 18.81 Hs.351005 252884 AF533251 zinc finger protein 396 ZNF436 7.11 Hs.293798 80818 AI829509 zinc finger protein 436 ZNF439 5.39 Hs.378527 90594 N29327 zinc finger protein 439 ZNF471 7.23 Hs.230188 57573 AL042523 zinc finger protein 471 ZNF533 8.23 Hs.6295 151126 BC038422 zinc finger protein 533 ZNF555 9.10 Hs.12471 148254 AF052118 zinc finger protein 555 ZNF7 8.09 Hs.2076 7553 194531 AI862153 zinc finger protein 7 (KOX 4, clone HF.16) 116.51 Hs.11873 AW167727 Transcribed sequences 66.25 Hs.177968 AI821586 Transcribed sequence with weak similarity to protein ref: NP_066928.1 (H. sapiens) phospholipid scramblase 1 [Homo sapiens] 54.91 Hs.160418 BF941609 Transcribed sequences 52.28 Hs.444751 AI916532 Transcribed sequences 50.21 Hs.390285 401221 BC034407 CDNA clone IMAGE: 5268504, partial cds 43.32 Hs.518877 BC014345 Clone IMAGE: 3935474, mRNA 42.12 Hs.446121 AW450381 Transcribed sequences 41.67 Hs.445324 BF513800 Transcribed sequences 40.16 Hs.514745 N63706 CDNA FLJ41084 fis, clone ADRGL2010974 35.98 Hs.434969 AI917371 Transcribed sequences 35.50 Hs.145404 345557 AI694325 Similar to RIKEN cDNA B130016O10 gene (LOC345557), mRNA 33.79 Hs.127462 AI190292 Transcribed sequences 33.43 Hs.50850 AI127440 CDNA FLJ30128 fis, clone BRACE1000124 32.63 Hs.348762 AI143879 CDNA FLJ25677 fis, clone TST04054 30.42 AI248055 Consensus includes gb: AI248055 /FEA = EST /DB_XREF = gi: 3843452 /DB_XREF = est: qh64c02.x1 /CLONE = IMAGE: 1849442 /UG = Hs.137263 ESTs 30.05 Hs.7888 AW772192 CDNA FLJ44318 fis, clone TRACH3000780 29.77 Hs.382051 BC014585 Clone IMAGE: 4047715, mRNA 29.74 Hs.446340 AW291402 Transcribed sequences 28.51 Hs.112742 401141 BF508344 CDNA clone IMAGE: 6301163, containing frame-shift errors 28.41 Hs.118317 AU147152 CDNA FLJ12088 fis, clone HEMBB1002545 27.71 Hs.360628 401154 AW873604 CDNA FLJ42757 fis, clone BRAWH3001712 24.86 Hs.158853 AW274369 Transcribed sequences 24.14 AF009316 gb: AF009316.1 /DB_XREF = gi: 2331119 /TID = Hs2.384893.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd / STK = 0 /UG = Hs.384893 /UG_TITLE = Homo sapiens clone TUB2 Cri-du-chat region mRNA /DEF = Homo sapiens clone TUB2 Cri-du-chat region mRNA. 24.04 Hs.531661 AF088010 Full length insert cDNA clone YY74E10 23.38 Hs.287436 AU145336 CDNA FLJ11655 fis, clone HEMBA1004554 22.75 Hs.106975 H10408 Transcribed sequences 21.99 BC037932 gb: BC037932.1 /DB_XREF = gi: 23138809 /TID = Hs2.385469.1 /CNT = 2 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.385469 /UG_TITLE = Homo sapiens, clone IMAGE: 5285165, mRNA /DEF = Homo sapiens, clone IMAGE: 5285165, mRNA. 21.26 Hs.451103 BC041486 CDNA clone IMAGE: 5492202, partial cds 20.96 Hs.269873 AF339813 Clone IMAGE: 297403, mRNA sequence 20.87 Hs.113150 AV739182 Transcribed sequences 20.10 Hs.191144 T83380 Transcribed sequences 19.98 Hs.525221 AW291482 Transcribed sequences 19.17 Hs.346735 BE222344 Clone IMAGE: 3881549, mRNA 18.97 Hs.256230 AW418842 CDNA FLJ31245 fis, clone KIDNE2005062 17.92 Hs.265194 BF223214 Transcribed sequences 17.65 Hs.523019 AI801626 Transcribed sequence with weak similarity to protein ref: NP_055301.1 (H. sapiens) neuronal thread protein [Homo sapiens] 16.87 Hs.121518 BE932011 Transcribed sequence with strong similarity to protein sp: P00722 (E. coli) BGAL_ECOLI Beta-galactosidase 16.53 Hs.126622 AW341701 Transcribed sequences 16.52 Hs.348682 401612 AL833609 Similar to mitochondrial carrier triple repeat 1 (LOC401612), mRNA 16.41 Hs.201875 BE645480 Transcribed sequences 16.35 Hs.296014 AU148154 CDNA FLJ14136 fis, clone MAMMA1002744 16.33 Hs.375762 AI955713 Clone IMAGE: 4828750, mRNA 16.33 Hs.390443 BC043538 Clone IMAGE: 5170153, mRNA 16.27 Hs.488530 AF086391 Full length insert cDNA clone ZD73H04 15.79 Hs.244283 AA018404 MRNA; cDNA DKFZp686I19109 (from clone DKFZp686I19109) 15.55 Hs.519952 AL833685 MRNA; cDNA DKFZp667O0522 (from clone DKFZp667O0522) 15.45 Hs.13188 AW300488 Human HepG2 partial cDNA, clone hmd5d04m5. 15.37 Hs.311250 AL137360 MRNA; cDNA DKFZp434C0326 (from clone DKFZp43400326) 15.33 Hs.96917 BF591483 Transcribed sequences 15.15 Hs.316856 BC040219 Clone IMAGE: 4818734, mRNA 15.15 Hs.505003 BG208091 CDNA FLJ37414 fis, clone BRAWH1000157 15.05 Hs.126995 BM969275 CDNA FLJ46728 fis, clone TRACH3019142 14.91 Hs.345792 AI684551 Transcribed sequence with weak similarity to protein ref: NP_077243.1 (M. musculus) ribosome binding protein 1 isoform mRRp61 [Mus musculus] 14.91 Hs.441051 AI769647 CDNA clone IMAGE: 5296106, partial cds 14.75 Hs.526642 H49805 Transcribed sequences 14.18 Hs.264606 AI741597 Full length insert cDNA clone ZD68B12 13.94 Hs.528540 401074 BC039495 Similar to double homeobox protein (LOC401074), mRNA 13.54 Hs.241559 AL109791 MRNA full length insert cDNA clone EUROIMAGE 151432 13.49 Hs.253690 BC042378 Clone IMAGE: 5277693, mRNA 13.17 Hs.291015 AA651631 Transcribed sequences 13.13 Hs.529285 AA588092 Transcribed sequences 12.65 Hs.128439 AI190306 Transcribed sequences 12.63 Hs.435959 BF511336 Transcribed sequences 12.55 Hs.202512 AI697714 Transcribed sequences 12.51 Hs.126918 R15004 Transcribed sequences 12.21 AL832724 gb: AL832724.1 /DB_XREF = gi: 21733304 /TID = Hs2.376962.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.376962 /UG_TITLE = Homo sapiens mRNA; cDNA DKFZp313I209 (from clone DKFZp313I209) /DEF = Homo sapiens mRNA; cDNA DKFZp313I209 (from clone DKFZp313I209). 12.16 Hs.385547 390845 BC036040 Similar to KIAA0563-related gene (LOC390845), mRNA 12.08 Hs.172778 AB046770 CDNA FLJ38287 fis, clone FCBBF3008362, moderately similar to PLEXIN 4 PRECURSOR 12.06 Hs.446559 BG024649 Transcribed sequence with strong similarity to protein sp: P00722 (E. coli) BGAL_ECOLI Beta-galactosidase 11.82 AK055534 gb: AK055534.1 /DB_XREF = gi: 16550279 /TID = Hs2.350858.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.350858 /UG_TITLE = Homo sapiens cDNA FLJ30972 fis, clone HEART2000492. /DEF = Homo sapiens cDNA FLJ30972 fis, clone HEART2000492. 11.80 Hs.348434 BC033956 Clone IMAGE: 5286779, mRNA 11.66 Hs.158528 BF002339 Transcribed sequences 11.58 Hs.110406 AI700341 Transcribed sequences 11.57 Hs.517745 AL359583 MRNA; cDNA DKFZp547L174 (from clone DKFZp547L174) 11.54 Hs.116462 AA639753 Transcribed sequences 11.28 Hs.28391 BF511741 CDNA FLJ37384 fis, clone BRAMY2026347 11.18 Hs.382361 BC034279 CDNA clone IMAGE: 4824424, containing frame-shift errors 11.17 Hs.143258 BC021687 Clone IMAGE: 3934974, mRNA 11.07 Hs.110286 AA418074 CDNA FLJ43404 fis, clone OCBBF2017516 10.97 Hs.194626 AA916568 Transcribed sequences 10.96 Hs.532249 AL833080 MRNA; cDNA DKFZp451G2119 (from clone DKFZp451G2119) 10.96 Hs.383399 AF113679 Clone FLB3107 10.87 Hs.108068 BF197757 Transcribed sequences 10.80 Hs.374838 AB002318 Clone 24641 mRNA sequence 10.70 AK024556 gb: AK024556.1 /DB_XREF = gi: 10436865 /TID = Hs2.383622.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.383622 /UG_TITLE = Homo sapiens cDNA: FLJ20903 fis, clone ADSE00222. /DEF = Homo sapiens cDNA: FLJ20903 fis, clone ADSE00222. 10.67 Hs.531632 R43486 CDNA FLJ33443 fis, clone BRALZ1000103 10.61 Hs.163734 BG028463 Transcribed sequences 10.54 Hs.143134 AW207243 CDNA FLJ38181 fis, clone FCBBF1000125 10.49 Hs.290853 AW970985 Transcribed sequences 10.43 Hs.447459 AU158588 CDNA FLJ13756 fis, clone PLACE3000365 10.37 Hs.525111 AW134504 Transcribed sequence with moderate similarity to protein sp: P39194 (H. sapiens) ALU7_HUMAN Alu subfamily SQ sequence contamination warning entry 10.34 AK096139 gb: AK096139.1 /DB_XREF = gi: 21755553 /TID = Hs2.376171.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.376171 /UG_TITLE = Homo sapiens cDNA FLJ38820 fis, clone LIVER2008473. /DEF = Homo sapiens cDNA FLJ38820 fis, clone LIVER2008473. 10.20 Hs.314414 BC040901 Clone IMAGE: 5743779, mRNA 10.15 Hs.432615 AW070877 Transcribed sequences 10.13 Hs.176872 AW297742 Transcribed sequences 10.05 AK057525 gb: AK057525.1 /DB_XREF = gi: 16553266 /TID = Hs2.401310.1 /CNT = 6 /FEA = mRNA /TIER = ConsEnd /STK = 5 /UG = Hs.401310 /UG_TITLE = Homo sapiens cDNA FLJ32963 fis, clone TESTI2008405. /DEF = Homo sapiens cDNA FLJ32963 fis, clone TESTI2008405. 9.91 BC016356 gb: BC016356.1 /DB_XREF = gi: 18921441 /TID = Hs2.382791.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.382791 /UG_TITLE = Homo sapiens, clone IMAGE: 4093039, mRNA /DEF = Homo sapiens, clone IMAGE: 4093039, mRNA. 9.90 Hs.283228 BC041378 CDNA clone IMAGE: 5274693, partial cds 9.85 Hs.521517 AY010114 Unknown mRNA sequence 9.74 Hs.16193 BG251521 MRNA; cDNA DKFZp586B211 (from clone DKFZp586B211) 9.64 Hs.116631 N63890 Transcribed sequences 9.59 Hs.130526 AI004009 Transcribed sequence with moderate similarity to protein sp: P39194 (H. sapiens) ALU7_HUMAN Alu subfamily SQ sequence contamination warning entry 9.50 Hs.176379 AA913023 Transcribed sequences 9.45 Hs.278177 AA809449 Transcribed sequence with weak similarity to protein sp: P39191 (H. sapiens) ALU4_HUMAN Alu subfamily SB2 sequence contamination warning entry 9.32 Hs.101428 AW628575 Transcribed sequences 9.25 Hs.373857 AA551114 Transcribed sequences 9.23 Hs.57773 AA449026 Transcribed sequences 9.09 Hs.46908 AI629041 Transcribed sequences 9.08 Hs.364332 BC042834 Clone IMAGE: 5314388, mRNA 9.00 Hs.22137 AI393695 MRNA; cDNA DKFZp686O0849 (from clone DKFZp686O0849) 8.94 Hs.508368 AF339805 Clone IMAGE: 248602, mRNA sequence 8.91 Hs.129620 AI970133 Transcribed sequences 8.84 Hs.481953 AU144883 CDNA FLJ11566 fis, clone HEMBA1003273 8.78 Hs.42522 255338 AI027091 Clone IMAGE: 4827791, mRNA 8.78 Hs.418040 BF476080 CDNA clone IMAGE: 30367357, partial cds 8.73 Hs.60797 AA017302 Transcribed sequences 8.70 Hs.114111 BM021056 Full length insert cDNA clone YA75D10 8.68 Hs.469666 AL041381 CDNA FLJ32512 fis, clone SMINT1000075 8.63 Hs.36958 AA496799 Transcribed sequences 8.59 Hs.212298 AW204033 Transcribed sequence with weak similarity to protein sp: P39189 (H. sapiens) ALU2_HUMAN Alu subfamily SB sequence contamination warning entry 8.57 Hs.365692 AL691692 CDNA FLJ20833 fis, clone ADKA02957 8.57 Hs.158209 BE178418 Transcribed sequence with weak similarity to protein ref: NP_062553.1 (H. sapiens) hypothetical protein FLJ11267 [Homo sapiens] 8.54 Hs.12533 Z39557 Clone 23705 mRNA sequence 8.50 Hs.499320 AU147518 CDNA FLJ12203 fis, clone MAMMA1000914 8.48 Hs.150378 BF063236 Transcribed sequences 8.47 Hs.306704 AK024800 CDNA: FLJ21147 fis, clone CAS09371 8.41 AL137313 Consensus includes gb: AL137313.1 /DEF = Homo sapiens mRNA; cDNA DKFZp761M10121 (from clone DKFZp761M10121). /FEA = mRNA /DB_XREF = gi: 6807798 /UG = Hs.306449 Homo sapiens mRNA; cDNA DKFZp761M10121 (from clone DKFZp761M10121) 8.41 AK098258 gb: AK098258.1 /DB_XREF = gi: 21758235 /TID = Hs2.379809.2 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.379809 /UG_TITLE = Homo sapiens cDNA FLJ40939 fis, clone UTERU2008077. /DEF = Homo sapiens cDNA FLJ40939 fis, clone UTERU2008077. 8.39 Hs.136672 BC043227 CDNA clone IMAGE: 5295530, partial cds 8.36 Hs.434253 BC042892 Clone IMAGE: 4830182, mRNA 8.36 Hs.351262 AI950472 Similar to otoconin 90, clone IMAGE: 4278507, mRNA 8.32 Hs.531627 400680 BE138486 MRNA; cDNA DKFZp686K1836 (from clone DKFZp686K1836) 8.31 Hs.249946 AV700086 Transcribed sequences 8.26 Hs.105500 AA521154 Transcribed sequences 8.24 Hs.444915 AI734054 Transcribed sequences 8.21 Hs.444387 AI051967 Transcribed sequences 8.18 Hs.384618 AF086084 Full length insert cDNA clone YZ84C01 8.18 Hs.370704 AW104813 CDNA FLJ36685 fis, clone UTERU2008018 8.11 Hs.192075 AA702409 Transcribed sequences 8.10 Hs.117474 R49146 CDNA FLJ34491 fis, clone HLUNG2004774 8.08 Hs.492671 AU147969 CDNA FLJ12341 fis, clone MAMMA1002269 8.07 Hs.421746 CA442689 CDNA FLJ13866 fis, clone THYRO1001213 8.05 Hs.126024 AL041122 Transcribed sequence with weak similarity to protein ref: NP_491607.1 (C. elegans) C09D4.4a.p [Caenorhabditis elegans] 8.03 Hs.527657 AL552727 Transcribed sequences 8.03 Hs.133319 BE675108 Alu repeat mRNA sequence 8.02 Hs.51515 AA053967 MRNA; cDNA DKFZp564G112 (from clone DKFZp564G112) 8.02 Hs.155814 N23033 Transcribed sequence with strong similarity to protein sp: P00722 (E. coli) BGAL_ECOLI Beta-galactosidase 7.98 Hs.98314 AL553774 MRNA; cDNA DKFZp586L0120 (from clone DKFZp586L0120) 7.93 Hs.408455 AA002022 MRNA; cDNA DKFZp686J1595 (from clone DKFZp686J1595) 7.91 Hs.488293 N74195 Transcribed sequence with weak similarity to protein ref: NP_079268.1 (H. sapiens) hypothetical protein FLJ12547 [Homo sapiens] 7.89 Hs.513302 N26569 MRNA; cDNA DKFZp686H0155 (from clone DKFZp686H0155) 7.88 Hs.287413 AU144140 CDNA FLJ11419 fis, clone HEMBA1000985 7.80 AF009316 gb: AF009316.1 /DB_XREF = gi: 2331119 /TID = Hs2.384893.1 /CNT = 1 /FEA = mRNA / TIER = ConsEnd /STK = 0 /UG = Hs.384893 /UG_TITLE = Homo sapiens clone TUB2 Cri-du-chat region mRNA /DEF = Homo sapiens clone TUB2 Cri-du-chat region mRNA. 7.75 Hs.475627 AU147983 CDNA FLJ43139 fis, clone CTONG3007444 7.71 Hs.526982 BE674460 Transcribed sequence with strong similarity to protein pir: S38965 (H. sapiens) S38965 mannosyl-oligosaccharide 1,2-alpha-mannosidase 7.70 Hs.407197 BC028204 Clone IMAGE: 5201079, mRNA 7.68 Hs.269924 BF435438 Full length insert cDNA YH93B03 7.67 Y16185 gb: Y16185.1 /DB_XREF = gi: 3176023 /TID = Hs2.382267.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.382267 /UG_TITLE = Homo sapiens partial mRNA, ID band56 /DEF = Homo sapiens partial mRNA, ID band56. 7.66 Hs.370466 AI939460 Transcribed sequences 7.64 Hs.459142 CA442342 Clone IMAGE: 5288686, mRNA 7.63 Hs.268597 AK025151 CDNA: FLJ21498 fis, clone COL05627 7.52 Hs.370312 AI953011 Transcribed sequences 7.51 Hs.277215 389659 BC028018 LOC389659 (LOC389659), mRNA 7.48 Hs.162518 D80168 MRNA; cDNA DKFZp686P21116 (from clone DKFZp686P21116) 7.42 Hs.118704 AI807197 Transcribed sequence with weak similarity to protein pir: I38022 (H. sapiens) I38022 hypothetical protein - human 7.35 Hs.517144 AK091704 CDNA FLJ34385 fis, clone HCHON1000142 7.34 AI142544 Consensus includes gb: AI142544 /FEA = EST /DB_XREF = gi: 3658903 /DB_XREF = est: qb47b03.x1 /CLONE = IMAGE: 1703213 /UG = Hs.158950 ESTs 7.29 Hs.377660 AI498395 CDNA FLJ26242 fis, clone DMC00770 7.28 Hs.434610 BC040327 Clone IMAGE: 4830466, mRNA 7.26 Hs.272033 T92908 Transcribed sequences 7.26 Hs.450057 344595 AI678088 Clone IMAGE: 5300025, mRNA 7.26 Hs.145331 AI252905 Transcribed sequences 7.24 AK057525 gb: AK057525.1 /DB_XREF = gi: 16553266 /TID = Hs2.401310.1 /CNT = 6 /FEA = mRNA /TIER = ConsEnd /STK = 5 /UG = Hs.401310 /UG_TITLE = Homo sapiens cDNA FLJ32963 fis, clone TESTI2008405. /DEF = Homo sapiens cDNA FLJ32963 fis, clone TESTI2008405. 7.22 AK093656 gb: AK093656.1 /DB_XREF = gi: 21752574 /TID = Hs2.232296.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.232296 /UG_TITLE = Homo sapiens cDNA FLJ36337 fis, clone THYMU2006324. /DEF = Homo sapiens cDNA FLJ36337 fis, clone THYMU2006324. 7.22 AI264125 Consensus includes gb: AI264125 /FEA = EST /DB_XREF = gi: 3872328 /DB_XREF = est: qk03a05.x1 /CLONE = IMAGE: 1867856 /UG = Hs.299056 ESTs 7.19 Hs.531773 AV703843 CDNA FLJ25185 fis, clone CBR09429 7.18 Hs.132571 AL049337 MRNA; cDNA DKFZp564P016 (from clone DKFZp564P016) 7.16 Hs.46689 AF088007 Full length insert cDNA clone YY74A01 7.12 Hs.371746 AI125516 Transcribed sequence with weak similarity to protein pir: VWHU (H. sapiens) VWHU von Willebrand factor precursor - human 7.07 Hs.105738 AA831943 Transcribed sequences 7.03 Hs.144469 AW663083 Clone IMAGE: 5285945, mRNA 7.03 Hs.469331 AU159040 CDNA FLJ13833 fis, clone THYRO1000676 7.01 Hs.26346 AI638405 CDNA FLJ42589 fis, clone BRACE3009701 7.00 Hs.362343 BF207861 CDNA FLJ41751 fis, clone HSYRA2008154 6.98 Hs.390736 R71245 Transcribed sequence with weak similarity to protein ref: NP_495786.1 (C. elegans) F22B5.10.p [Caenorhabditis elegans] 6.96 Hs.147030 AI186173 Transcribed sequence with moderate similarity to protein sp: P00722 (E. coli) BGAL_ECOLI Beta-galactosidase 6.96 Hs.287562 AK023375 CDNA FLJ13313 fis, clone OVARC1001489 6.91 Hs.37902 AI808348 Transcribed sequences 6.88 Hs.21248 R40515 Transcribed sequences 6.83 Hs.12853 BF446943 MRNA; cDNA DKFZp762M127 (from clone DKFZp762M127) 6.81 Hs.99836 AI384076 MRNA; cDNA DKFZp686B0610 (from clone DKFZp686B0610) 6.79 Hs.357304 AW103823 Clone IMAGE: 5266114, mRNA 6.76 AF334792 gb: AF334792.1 /DEF = Homo sapiens P143 mRNA, complete cds. /FEA = mRNA /PROD = P143 /DB_XREF = gi: 12659333 /UG = Hs.307005 Homo sapiens P143 mRNA, complete cds /FL = gb: AF334792.1 6.75 Hs.508096 AU157457 CDNA FLJ11204 fis, clone PLACE1007810 6.73 Hs.407118 AL833266 MRNA; cDNA DKFZp451G0810 (from clone DKFZp451G0810) 6.72 Hs.526497 BC040539 Clone IMAGE: 5267024, mRNA 6.68 Hs.405427 AI283051 Clone IMAGE: 5175565, mRNA 6.68 Hs.201184 BE551395 Transcribed sequence with weak similarity to protein ref: NP_060265.1 (H. sapiens) hypothetical protein FLJ20378 [Homo sapiens] 6.65 AF086490 gb: AF086490.1 /DB_XREF = gi: 3483835 /TID = Hs2.384576.1 /CNT = 2 /FEA = mRNA /TIER = ConsEnd /STK = 1 /UG = Hs.384576 /UG_TITLE = Homo sapiens full length insert cDNA clone ZD94H12. /DEF = Homo sapiens full length insert cDNA clone ZD94H12 6.65 Hs.144759 AI200555 CDNA FLJ32438 fis, clone SKMUS2001402 6.63 BC039119 gb: BC039119.1 /DB_XREF = gi: 24659569 /TID = Hs2.407561.1 /CNT = 2 /FEA = mRNA /TIER = ConsEnd /STK = 1 /UG = Hs.407561 /UG_TITLE = Homo sapiens, clone IMAGE: 4838391, mRNA /DEF = Homo sapiens, clone IMAGE: 4838391, mRNA. 6.61 Hs.9887 AI683805 CDNA FLJ36309 fis, clone THYMU2004986 6.60 Hs.445500 AI225238 Transcribed sequences 6.55 Hs.383205 BE276551 Clone IMAGE: 3050253, mRNA 6.54 Hs.484965 AA766296 MRNA; cDNA DKFZp686P16118 (from clone DKFZp686P16118) 6.52 Hs.487431 AA554430 CDNA FLJ14343 fis, clone THYRO1000916 6.50 Hs.58423 AF086424 Full length insert cDNA clone ZD78G02 6.49 AL117528 Consensus includes gb: AL117528.1 /DEF = Homo sapiens mRNA; cDNA DKFZp434P2450 (from clone DKFZp434P2450). /FEA = mRNA /DB_XREF = gi: 5912054 /UG = Hs.306350 Homo sapiens mRNA; cDNA DKFZp434P2450 (from clone DKFZp434P2450) 6.48 Hs.169068 AU144005 CDNA FLJ11397 fis, clone HEMBA1000622 6.47 Hs.61590 AI300077 Transcribed sequences 6.43 Hs.369777 401176 BC043001 Clone IMAGE: 5297432, mRNA 6.42 AF314543 gb: AF314543.1 /DEF = Homo sapiens ovarian cancer-related protein 1 (OCR1) mRNA, complete cds. /FEA = mRNA /GEN = OCR1 /PROD = ovarian cancer-related protein 1 /DB_XREF = gi: 12584148 /UG = Hs.307048 Homo sapiens ovarian cancer-related protein 1 (OCR1) mRNA, . . . 6.41 Hs.21965 AI798981 Clone IMAGE: 4813782, mRNA 6.39 NM_025089 gb: NM_025089.1 /DEF = Homo sapiens hypothetical protein FLJ23497 (FLJ23497), mRNA. /FEA = mRNA /GEN = FLJ23497 /PROD = hypothetical protein FLJ23497 /DB_XREF = gi: 13376647 /UG = Hs.288498 hypothetical protein FLJ23497 /FL = gb: NM_025089.1 6.36 Hs.130203 AW301241 Transcribed sequences 6.35 Hs.434203 BC042835 Clone IMAGE: 4828037, mRNA 6.35 AL137305 Consensus includes gb: AL137305.1 /DEF = Homo sapiens mRNA; cDNA DKFZp434J197 (from clone DKFZp434J197). /FEA = mRNA /DB_XREF = gi: 6807770 /UG = Hs.306447 Homo sapiens mRNA; cDNA DKFZp434J197 (from clone DKFZp434J197) 6.34 Hs.149442 AI346891 Transcribed sequences 6.32 Hs.385767 BC038784 Clone IMAGE: 5271697, mRNA 6.28 Hs.391856 BG150301 CDNA FLJ42567 fis, clone BRACE3007559 6.24 Hs.306566 AF090948 Clone HQ0709 6.22 Hs.385614 BC035176 Clone IMAGE: 5266012, mRNA 6.21 Hs.436589 BC041341 Clone IMAGE: 5272066, mRNA 6.20 Hs.136941 AW182342 Transcribed sequences 6.20 Hs.372303 AW611685 CDNA FLJ45450 fis, clone BRSTN2002691 6.19 Hs.17892 AA411712 Transcribed sequences 6.18 Hs.133386 AI056872 Transcribed sequences 6.15 Hs.353387 AL832704 MRNA; cDNA DKFZp313A1935 (from clone DKFZp313A1935) 6.14 Hs.22542 N49237 Clone IMAGE: 5312516, mRNA 6.09 Hs.385747 BC038195 Clone IMAGE: 3918875, mRNA 6.07 Hs.49774 AI040744 Transcribed sequences 6.06 Hs.102981 AL122040 CDNA FLJ43416 fis, clone OCBBF2025730 6.05 Hs.382138 400234 BC029835 CDNA FLJ27344 fis, clone TST03461 6.02 Hs.529382 BG236742 Transcribed sequences 6.01 Hs.481773 AK095656 CDNA FLJ38337 fis, clone FCBBF3026692 6.01 Hs.133107 AW271932 Transcribed sequences 6.01 BC037921 gb: BC037921.1 /DB_XREF = gi: 23138806 /TID = Hs2.385471.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.385471 /UG_TITLE = Homo sapiens, clone IMAGE: 5278633, mRNA /DEF = Homo sapiens, clone IMAGE: 5278633, mRNA. 6.00 Hs.270027 AI683911 Transcribed sequence with weak similarity to protein sp: P39194 (H. sapiens) ALU7_HUMAN Alu subfamily SQ sequence contamination warning entry 5.99 Hs.283417 AI826437 Transcribed sequences 5.99 Hs.365415 BC037799 Clone IMAGE: 4792036, mRNA 5.97 Hs.434573 BQ184537 Full length insert cDNA clone ZB72E12 5.97 Hs.112916 BF445273 Transcribed sequences 5.96 Hs.530006 BG436225 CDNA FLJ35202 fis, clone PLACE6018287 5.95 Hs.519717 BM668595 CDNA FLJ33578 fis, clone BRAMY2011639 5.95 Hs.173400 BF724303 Transcribed sequences 5.95 Hs.27621 BF940761 CDNA FLJ12815 fis, clone NT2RP2002546 5.94 Hs.326721 AF339788 Clone IMAGE: 208561, mRNA sequence 5.93 BC043264 gb: BC043264.1 /DB_XREF = gi: 27695862 /TID = Hs2.434164.1 /CNT = 2 /FEA = mRNA /TIER = ConsEnd /STK = 1 /UG = Hs.434164 /UG_TITLE = Homo sapiens, clone IMAGE: 5296753, mRNA /DEF = Homo sapiens, clone IMAGE: 5296753, mRNA. 5.92 Hs.406798 AU144676 CDNA FLJ11533 fis, clone HEMBA1002678 5.90 Hs.128024 392659 AI798822 CDNA FLJ27139 fis, clone SPL08682 5.90 Hs.130370 AI130988 Transcribed sequences 5.88 Hs.370869 AW173212 Transcribed sequences 5.86 Hs.71947 AA565852 MRNA full length insert cDNA clone EUROIMAGE 994183 5.86 Hs.201980 400516 AI914160 Hypothetical gene supported by AK126852 (LOC400516), mRNA 5.84 Hs.12473 AF052109 Clone 23927 mRNA sequence 5.83 Hs.115122 AA228366 Transcribed sequences 5.83 AU144309 Consensus includes gb: AU144309 /FEA = EST /DB_XREF = gi: 11005830 /DB_XREF = est: AU144309 /CLONE = HEMBA1001533 /UG = Hs.55830 Homo sapiens cDNA FLJ10068 fis, clone HEMBA1001533 5.81 Hs.368488 AA476583 Transcribed sequences 5.81 Hs.362707 400648 BC031271 Hypothetical gene supported by BC031271 (LOC400648), mRNA 5.78 AF257500 gb: AF257500.1 /DEF = Homo sapiens SYTSSX4 fusion protein (SSXTSSX4 fusion) mRNA, complete cds. /FEA = mRNA /GEN = SSXTSSX4 fusion /PROD = SYTSSX4 fusion protein /DB_XREF = gi: 11127694 /UG = Hs.289105 synovial sarcoma, X breakpoint 2 /FL = gb: AF257500.1 . . . 5.78 Hs.445792 BC037349 Clone IMAGE: 5266332, mRNA 5.77 Hs.375821 BC031963 Clone IMAGE: 4838328, mRNA 5.77 AA905023 Consensus includes gb: AA905023 /FEA = EST /DB_XREF = gi: 3040146 /DB_XREF = est: ok09c06.s1 /CLONE = IMAGE: 1507306 /UG = Hs.130769 ESTs 5.76 Hs.380219 BC034696 MRNA similar to RIKEN cDNA A030009B12 gene (cDNA clone MGC: 21382 IMAGE: 4746351), complete cds 5.75 AK027174 Consensus includes gb: AK027174.1 /DEF = Homo sapiens cDNA: FLJ23521 fis, clone LNG04928. /FEA = mRNA /DB_XREF = gi: 10440240 /UG = Hs.306909 Homo sapiens cDNA: FLJ23521 fis, clone LNG04928 5.75 Hs.406106 BG149337 Transcribed sequences 5.74 Hs.200004 AI808303 Transcribed sequences 5.72 Hs.381113 AW576443 Transcribed sequences 5.72 Hs.526474 BC000856 CDNA: FLJ21331 fis, clone COL02520 5.71 Hs.62929 AI083557 CDNA FLJ42179 fis, clone THYMU2030796 5.71 Hs.243596 AI807482 MRNA; cDNA DKFZp686I21166 (from clone DKFZp686I21166) 5.70 Hs.100636 AW960145 CDNA FLJ36210 fis, clone THYMU2000155 5.70 Hs.438377 AK023938 CDNA FLJ13876 fis, clone THYRO1001401 5.68 Hs.280216 BF510506 Transcribed sequence with weak similarity to protein sp: P08547 (H. sapiens) LIN1_HUMAN LINE-1 REVERSE TRANSCRIPTASE HOMOLOG 5.68 Hs.201953 Y10204 H. sapiens mRNA for CD77 protein 5.67 Hs.257683 AW572853 Transcribed sequence with moderate similarity to protein sp: P39190 (H. sapiens) ALU3_HUMAN Alu subfamily SB1 sequence contamination warning entry 5.66 Hs.401142 AL832260 MRNA; cDNA DKFZp667G1817 (from clone DKFZp667G1817) 5.65 Hs.308222 402476 BI823265 CDNA FLJ46106 fis, clone TESTI2026284 5.65 Hs.375072 BC030740 CDNA clone IMAGE: 4791521, partial cds 5.64 Hs.429375 AI272805 Transcribed sequences 5.62 D00267 Consensus includes gb: D00267 /DEF = Homo sapiens pseudogene for cytochrome c-like protein, clone pHGC4E1 /FEA = CDS /DB_XREF = gi: 219559 /UG = Hs.248014 Homo sapiens pseudogene for cytochrome c-like protein, clone pHGC4E1 5.61 AI990495 Consensus includes gb: AI990495 /FEA = EST /DB_XREF = gi: 5837376 /DB_XREF = est: ws40d02.x1 /CLONE = IMAGE: 2499651 /UG = Hs.126809 ESTs 5.60 Hs.130260 AI695695 Transcribed sequences 5.55 Hs.107070 H93043 Transcribed sequences 5.54 Hs.501925 AU144382 CDNA FLJ11476 fis, clone HEMBA1001745 5.54 Hs.98073 AA490685 CDNA: FLJ22994 fis, clone KAT11918 5.53 Hs.126133 389324 AI799695 MRNA; cDNA DKFZp686D0374 (from clone DKFZp686D0374) 5.52 Hs.262826 AI218551 Transcribed sequences 5.51 Hs.373571 AA305027 CDNA FLJ39665 fis, clone SMINT2007294 5.50 Hs.445122 AW291140 Transcribed sequences 5.48 NM_025116 gb: NM_025116.1 /DEF = Homo sapiens hypothetical protein FLJ12781 (FLJ12781), mRNA. /FEA = mRNA /GEN = FLJ12781 /PROD = hypothetical protein FLJ12781 /DB_XREF = gi: 13376692 /UG = Hs.288726 hypothetical protein FLJ12781 /FL = gb: NM_025116.1 5.48 Hs.7309 AA995925 CDNA FLJ34019 fis, clone FCBBF2002898 5.48 Hs.268818 AF147404 Full length insert cDNA clone YP01H07 5.47 Hs.433791 AW664964 Transcribed sequence with weak similarity to protein ref: NP_060312.1 (H. sapiens) hypothetical protein FLJ20489 [Homo sapiens] 5.46 Hs.432355 392551 AI080106 Similar to Ras-related protein Rab-28 (Rab-26) (LOC392551), mRNA 5.46 Hs.302631 AW952781 CDNA clone IMAGE: 5286843, partial cds 5.45 Hs.371751 BC044305 Clone IMAGE: 5174069, mRNA 5.44 Hs.434569 BQ707702 Full length insert cDNA clone YB66H06 5.44 Hs.523914 AI565746 Full length insert cDNA YH73H08 5.44 Hs.185701 AL109696 MRNA full length insert cDNA clone EUROIMAGE 21920 5.42 Hs.16370 AW139789 CDNA FLJ11652 fis, clone HEMBA1004461 5.41 Hs.371436 AW418647 CDNA FLJ34002 fis, clone FCBBF1000206 5.41 Hs.160900 BI560014 CDNA FLJ39420 fis, clone PLACE6018769 5.41 Hs.96297 AI051769 Transcribed sequence with weak similarity to protein ref: NP_055301.1 (H. sapiens) neuronal thread protein [Homo sapiens] 5.39 Hs.356457 AW197431 Transcribed sequence with moderate similarity to protein sp: P39194 (H. sapiens) ALU7_HUMAN Alu subfamily SQ sequence contamination warning entry 5.39 BE066040 Consensus includes gb: BE066040 /FEA = EST /DB_XREF = gi: 8410690 /DB_XREF = est: RC3-BT0319-240200-015-c01 /UG = Hs.292358 ESTs 5.38 Hs.448887 AF131798 Clone 25119 mRNA sequence 5.37 Hs.407471 BC034815 CDNA FLJ25418 fis, clone TST03512 5.35 Hs.4194 AK024956 CDNA: FLJ21303 fis, clone COL02107 5.35 Hs.432643 AK001829 CDNA FLJ10967 fis, clone PLACE1000798 5.35 Hs.470154 AK026778 CDNA: FLJ23125 fis, clone LNG08217 5.34 Hs.28803 BE501976 Transcribed sequence with moderate similarity to protein sp: P39192 (H. sapiens) ALU5_HUMAN Alu subfamily SC sequence contamination warning entry 5.34 Hs.531894 BC036311 Clone IMAGE: 4819526, mRNA 5.34 Hs.105623 AI038071 Transcribed sequences 5.33 Hs.190060 AI874267 Transcribed sequences 5.32 Hs.452398 AL037998 CDNA FLJ30740 fis, clone FEBRA2000319 5.31 Hs.356888 AL713714 MRNA; cDNA DKFZp667C0715 (from clone DKFZp667C0715) 5.31 Hs.502632 AK000995 CDNA FLJ10133 fis, clone HEMBA1003067 5.30 AF118079 gb: AF118079.1 /DEF = Homo sapiens PRO1854 mRNA, complete cds. /FEA = mRNA /PROD = PRO1854 /DB_XREF = gi: 6650803 /UG = Hs.136570 PRO1854 protein /FL = gb: AF118079.1 5.30 Hs.306439 AL122039 MRNA; cDNA DKFZp434E0572 (from clone DKFZp434E0572) 5.30 Hs.437104 AW139588 Transcribed sequences 5.30 Hs.13818 BE675486 Transcribed sequences 5.29 Hs.55378 AI123586 Transcribed sequences 5.29 Hs.105268 BC043176 CDNA clone IMAGE: 5287441, partial cds 5.27 Hs.133160 401237 H14782 Clone IMAGE: 5742072, mRNA 5.25 Hs.225986 AL050145 MRNA; cDNA DKFZp586C2020 (from clone DKFZp586C2020) 5.25 Hs.416521 BC039533 Clone IMAGE: 5743964, mRNA 5.25 Hs.178803 AA913383 Transcribed sequences 5.25 Hs.88156 BF207870 Transcribed sequences 5.25 Hs.406781 AL137325 MRNA; cDNA DKFZp434M0835 (from clone DKFZp434M0835) 5.23 Hs.355404 AW590614 Transcribed sequences 5.22 Hs.252588 AL359626 MRNA; cDNA DKFZp564F172 (from clone DKFZp564F172) 5.21 Hs.126895 AA932539 Transcribed sequences 5.21 Hs.291564 BE467383 Transcribed sequence with moderate similarity to protein sp: P39194 (H. sapiens) ALU7_HUMAN Alu subfamily SQ sequence contamination warning entry 5.21 Hs.197745 AI660254 Transcribed sequences 5.21 Hs.28540 AL050204 MRNA; cDNA DKFZp586F1223 (from clone DKFZp586F1223) 5.20 Hs.400256 AW162768 CDNA FLJ11478 fis, clone HEMBA1001781 5.18 Hs.272198 AK000798 CDNA FLJ20791 fis, clone COL01392 5.18 U54734 gb: U54734.1 /DB_XREF = gi: 2724997 /TID = Hs2.384853.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 1 /UG = Hs.384853 /UG_TITLE = Human clone TM029 mRNA sequence. /DEF = Human clone TM029 mRNA sequence. 5.16 AF143866 gb: AF143866.1 /DB_XREF = gi: 4895008 /TID = Hs2.407308.1 /CNT = 2 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.407308 /UG_TITLE = Homo sapiens clone IMAGE: 110987 mRNA sequence /DEF = Homo sapiens clone IMAGE: 110987 mRNA sequence. 5.15 Hs.252924 AA883831 Transcribed sequences 5.14 Hs.282340 AV646408 Transcribed sequences 5.14 Hs.174067 AI401627 Transcribed sequences 5.13 Hs.439326 AU145365 CDNA FLJ11662 fis, clone HEMBA1004629 5.12 Hs.43744 AW290940 CDNA FLJ35131 fis, clone PLACE6008824 5.11 Hs.308017 AI125337 CDNA FLJ36973 fis, clone BRACE2006249 5.11 Hs.375788 AL713719 MRNA; cDNA DKFZp667K1916 (from clone DKFZp667K1916) 5.09 X79200 Consensus includes gb: X79200.1 /DEF = Homo spaiens mRNA for SYT-SSX protein. /FEA = mRNA /PROD = SYT-SSX protein /DB_XREF = gi: 531107 /UG = Hs.289105 synovial sarcoma, X breakpoint 2 5.08 Hs.376811 AL833811 MRNA; cDNA DKFZp564G203 (from clone DKFZp564G203) 5.08 Hs.531959 BC040680 Clone IMAGE: 4817893, mRNA 5.08 AK024527 gb: AK024527.1 /DB_XREF = gi: 10436829 /TID = Hs2.306684.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.306684 /UG_TITLE = Homo sapiens cDNA: FLJ20874 fis, clone ADKA02818. /DEF = Homo sapiens cDNA: FLJ20874 fis, clone ADKA02818. 5.07 Hs.385644 BC023608 CDNA clone IMAGE: 4639754, partial cds 5.06 Hs.493477 AW301393 CDNA FLJ10263 fis, clone HEMBB1000991 5.05 Hs.445316 BF509230 Transcribed sequences 5.05 Hs.434344 BC041884 Clone IMAGE: 5298352, mRNA 5.02 Hs.274593 AL162033 MRNA; cDNA DKFZp434F1872 (from clone DKFZp434F1872) 5.02 Hs.531897 AV700891 Transcribed sequences 5.01 Hs.282377 AV647958 Transcribed sequences 5.01 Hs.144510 BF110426 Transcribed sequences 5.00 AL834280 gb: AL834280.1 /DB_XREF = gi: 21739855 /TID = Hs2.407106.1 /CNT = 1 /FEA = mRNA /TIER = ConsEnd /STK = 0 /UG = Hs.407106 /UG_TITLE = Homo sapiens mRNA; cDNA DKFZp547J0114 (from clone DKFZp547J0114) /DEF = Homo sapiens mRNA; cDNA DKFZp547J0114 (from clone DKFZp547J0114).

Increased expression of these cell surface markers in definitive endoderm cells as compared to hESCs was confirmed with real time QPCR as previously described. FIGS. 34A-M show the results of QPCR for certain markers. Results are displayed for cell cultures analyzed 1, 3 and 5 days after the addition of 100 ng/ml activin A, CXCR4-expressing definitive endoderm cells purified at the end of the five day differentiation procedure (CXDE), and in purified human embryonic stem cells (HESC). A comparison of FIGS. 34C and G-M demonstrates that the six marker genes, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1, exhibit an expression pattern that is almost identical to each other and which is also identical to the pattern of expression of CXCR4 and SOX17/SOX7. As described previously, SOX17 is expressed in both the definitive endoderm as well as in the SOX7-expressing extra-embryonic endoderm. Since SOX7 is not expressed in the definitive endoderm, the ratio of SOX17/SOX7 provides a reliable estimate of definitive endoderm contribution to the SOX17 expression witnessed in the population as a whole. The similarity of panels G-L and M to panel C indicates that FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1 are likely markers of definitive endoderm and that they are not significantly expressed in extra-embryonic endoderm cells. It will be appreciated that the Q-PCR results described herein can be further confirmed by ICC.

Table 4 describes a subset of genes included in Table 3 that exhibit over 30-fold upward change in expression in definitive endoderm cells as compared to hESCs. Select genes were assayed by Q-PCR, as described above, to verify the gene expression changes found on the gene chip and also to investigate the expression pattern of the genes during a during a time course of hESC differentiation as discussed below. Q-PCR data is presented in the column entitled “QPCR Fold Change,” where applicable.

TABLE 4 Highly up-regulated markers in definitive endoderm Raw Fold QPCR Fold Gene_Symbol Change Change Unigene LocusLink OMIM SeqDerivedFrom Gene Descriptor AGPAT3 53.81 Hs.443657 56894 AI337300 1-acylglycerol-3-phosphate O-acyltransferase 3 APOA2 33.51 47 Hs.237658 336 107670 NM_001643 apolipoprotein A-II C20orf56 36.01 140828 AL121722 chromosome 20 open reading frame 56 C21orf129 77.87 Hs.350679 150135 NM_152506 chromosome 21 open reading frame 129 CALCR 38.31 Hs.640 799 114131 NM_001742 calcitonin receptor CCL2 111.46 Hs.303649 6347 158105 S69738 chemokine (C-C motif) ligand 2 CER1 33.04 Hs.248204 9350 603777 NM_005454 cerberus 1 homolog, cysteine knot superfamily (Xenopus laevis) CMKOR1 53.39 213 Hs.231853 57007 AI817041 chemokine orphan receptor 1 CRIP1 50.56 28 1396 123875 NM_001311 cysteine-rich protein 1 (intestinal) CXCR4 55.31 289 Hs.421986 7852 162643 AJ224869 chemokine (C-X-C motif) receptor 4 CXorf1 54.35 Hs.106688 9142 NM_004709 chromosome X open reading frame 1 DIO3 33.07 Hs.49322 1735 601038 NM_001362 deiodinase, iodothyronine, type III DIO3OS 59.10 Hs.406958 64150 608523 AF305836 deiodinase, iodothyronine, type III opposite strand EB-1 162.04 Hs.372732 56899 607815 AW005572 E2a-Pbx1-associated protein EHHADH 85.52 Hs.432443 1962 607037 NM_001966 enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase ELOVL2 70.71 Hs.246107 54898 BF508639 elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2 EPSTI1 34.25 Hs.343800 94240 607441 AA633203 epithelial stromal interaction 1 (breast) FGF17 107.07 166 Hs.248192 8822 603725 NM_003867 fibroblast growth factor 17 FLJ10970 50.86 Hs.173233 55273 NM_018286 hypothetical protein FLJ10970 FLJ21195 83.56 Hs.207407 64388 BF064262 protein related to DAN and cerberus FLJ22471 34.33 Hs.387266 80212 NM_025140 limkain beta 2 FLJ23514 46.65 Hs.144913 60494 NM_021827 hypothetical protein FLJ23514 FOXA2 252.32 Hs.155651 3170 600288 AB028021 forkhead box A2 FOXQ1 43.02 85 Hs.297452 94234 AI676059 forkhead box Q1 GATA4 44.12 140 Hs.243987 2626 600576 AV700724 GATA binding protein 4 GPR37 33.44 Hs.406094 2861 602583 U87460 G protein-coupled receptor 37 (endothelin receptor type B-like) GSC 524.27 596 Hs.440438 145258 138890 AY177407 goosecoid LOC283537 68.29 Hs.117167 283537 AK026720 hypothetical protein LOC283537 MYL7 38.38 Hs.75636 58498 NM_021223 myosin, light polypeptide 7, regulatory NPPB 35.43 Hs.219140 4879 600295 NM_002521 natriuretic peptide precursor B NTN4 57.13 Hs.102541 59277 AF278532 netrin 4 PRSS2 205.03 Hs.511525 5645 601564 NM_002771 protease, serine, 2 (trypsin 2) RTN4RL1 60.66 Hs.22917 146760 H06251 reticulon 4 receptor-like 1 SEMA3E 135.96 Hs.528721 9723 NM_012431 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E SIAT8D 161.93 Hs.308628 7903 602547 AI422986 sialyltransferase 8D (alpha-2, 8-polysialyltransferase) SLC5A9 79.96 Hs.37890 200010 AI767388 solute carrier family 5 (sodium/glucose cotransporter), member 9 SLC40A1 44.06 Hs.409875 30061 604653 AL136944 solute carrier family 40 (iron-regulated transporter), member 1 SOX17 30.20 61 Hs.98367 64321 NM_022454 SRY (sex determining region Y)-box 17 SPOCK3 62.58 Hs.159425 50859 607989 AI808090 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3 TMOD1 74.09 Hs.374849 7111 190930 NM_003275 tropomodulin 1 TRPA1 103.37 Hs.137674 8989 604775 AA502609 transient receptor potential cation channel, subfamily A, member 1 TTN 76.16 Hs.434384 7273 188840 NM_003319 titin 116.51 Hs.11873 AW167727 Transcribed sequences 66.25 Hs.177968 AI821586 Transcribed sequence with weak similarity to protein ref: NP_066928.1 (H. sapiens) phospholipid scramblase 1 [Homo sapiens] 54.91 Hs.160418 BF941609 Transcribed sequences 52.28 Hs.444751 AI916532 Transcribed sequences 50.21 Hs.390285 401221 BC034407 CDNA clone IMAGE: 5268504, partial cds 40.16 Hs.514745 N63706 CDNA FLJ41084 fis, clone ADRGL2010974 30.05 Hs.7888 AW772192 CDNA FLJ44318 fis, clone TRACH3000780

Gene products that appear to be localized to the cell surface are described in Table 5. Localization of markers at the cell surface is useful for applications such as enrichment, isolation and/or purification of definitive endoderm cells. Each of the markers described in Table 5 include over a 30-fold increase in expression level in definitive endoderm as compared to hESCs.

TABLE 5 Up-regulated cell Surface markers in definitive endoderm Raw Fold QPCR Fold Gene_Symbol Change Change Unigene LocusLink OMIM SeqDerivedFrom Gene Descriptor CALCR 38.31 Hs.640 799 114131 NM_001742 calcitonin receptor CMKOR1 53.39 213 Hs.231853 57007 AI817041 chemokine orphan receptor 1 CXCR4 55.31 289 Hs.421986 7852 162643 AJ224869 chemokine (C-X-C motif) receptor 4 GPR37 33.44 Hs.406094 2861 602583 U87460 G protein-coupled receptor 37 (endothelin receptor type B-like) NTN4 57.13 Hs.102541 59277 AF278532 netrin 4 RTN4RL1 60.66 Hs.22917 146760 H06251 reticulon 4 receptor-like 1 SEMA3E 135.96 Hs.528721 9723 NM_012431 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E SLC5A9 79.96 Hs.37890 200010 AI767388 solute carrier family 5 (sodium/glucose cotransporter), member 9 SLC40A1 44.06 Hs.409875 30061 604653 AL136944 solute carrier family 40 (iron-regulated transporter), member 1 TRPA1 103.37 Hs.137674 8989 604775 AA502609 transient receptor potential cation channel, subfamily A, member 1

Example 12 Validation of Definitive Endoderm Markers

Using the methods, such as those described in the above Examples, hESCs are differentiated to produce definitive endoderm. In particular, to increase the yield and purity of definitive endoderm in differentiating cell cultures, the serum concentration of the medium is controlled as follows: 0% FBS on day 1, 0.2% FBS on day 2 and 2.0% FBS on days 3-6. Differentiating cell populations are grown in the presence of 100 ng/ml activin A, whereas non-differentiating control populations are grown in the absence of activin A. Human embryonic cell cultures grown in the presence or absence of activin A and in either 2% serum or 10% serum over the entire 6 day differentiation period are also monitored. Daily samples of each culture are withdrawn and the amount of mRNA transcript produced for each of the markers AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is measured by Q-PCR.

In general, expression levels of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 are high in cultures treated with 100 ng/ml activin A and low in those which do not receive exogenous activin A. Additionally, among activin A treated cultures, expression levels of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 are highest when FBS concentration is lowest. A decrease in AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 expression levels is seen in the 10% FBS cultures as compared to such expression levels in low serum FSB cultures.

Additionally, the expression profile of AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 is consistent with the expression profile of SOX17 and/or CXCR4 under similar conditions over the differentiation period.

The markers AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and AW772192 are not substantially expressed in cultures that are allowed to differentiate to mesoderm, ectoderm, or extra-embryonic endoderm.

Example 13 Isolation of Definitive Endoderm Cells using Markers Selected from Table 5

This Example demonstrates the isolation of definitive endoderm cells positive for AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and/or AW772192 in a cell culture by using a cell surface marker selected from CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1.

Using methods, such as those described in the above Examples, hESCs are differentiated to produce definitive endoderm. In particular, to increase yield and purity of definitive endoderm in differentiating cell cultures, the serum concentration of the medium is controlled as follows: 0% FBS on day 1, 0.2% FBS on day 2 and 2.0% FBS on days 3-6. Differentiating cell populations are grown in the presence of 100 ng/ml, 50 ng/ml or 25 ng/ml activin A, whereas non-differentiating control populations are grown in the absence of activin A.

An appropriate amount of labeled antibody that binds to one of the markers listed above is added to a sample of each culture and labeling proceeds on ice. Cells are washed by adding PBS and pelleted. A second wash with buffer is completed then cells are resuspended. Secondary antibody (FITC conjugated secondary antibody is added and allowed to label for about 30 minutes followed by two washes in buffer as above. Cells are resuspended and analyzed and sorted using a FACS. Cells are collected directly into RLT lysis buffer for subsequent isolation of total RNA for gene expression analysis by real-time quantitative PCR.

The number of cells positive for AGPAT3, APOA2, C20orf56, C21orf129, CALCR, CCL2, CER1, CMKOR1, CRIP1, CXCR4, CXorf1, DIO3, DIO3OS, EB-1, EHHADH, ELOVL2, EPSTI1, FGF17, FLJ10970, FLJ21195, FLJ22471, FLJ23514, FOXA2, FOXQ1, GATA4, GPR37, GSC, LOC283537, MYL7, NPPB, NTN4, PRSS2, RTN4RL1, SEMA3E, SIAT8D, SLC5A9, SLC40A1, SOX17, SPOCK3, TMOD1, TRPA1, TTN, AW166727, AI821586, BF941609, AI916532, BC034407, N63706 and/or AW772192 increase significantly as the dose of activin A is increased in the differentiation culture media. Isolated cell populations are analyzed as described in the Example below.

Example 14 Quantitation of Isolated Definitive Endoderm Cells

To quantitate the proportion of definitive endoderm cells present in a cell culture or cell population, cells expressing a cell surface marker selected from CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1 and other markers of definitive endoderm are analyzed by FACS.

Using the methods such as those described in the above Examples, hESCs are differentiated to produce definitive endoderm. In particular, to increase yield and purity of definitive endoderm in differentiating cell cultures, the serum concentration of the medium is controlled as follows: 0% FBS on day 1, 0.2% FBS on day 2 and 2.0% FBS on days 3-6. Differentiated cultures are sorted by FACS using cell surface epitopes, E-Cadherin, Thrombomodulin and one of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SEMA3E, SLC40A1, SLC5A9 and TRPA1 as described above. Sorted cell populations are then analyzed by Q-PCR to determine relative expression levels of markers for definitive and extraembryonic endoderm as well as other cell types. Use of any one of the above cell surface markers for isolation results in populations of definitive endoderm cells that are >98% pure.

Example 15 Transplantation of Human Definitive Endoderm Cells Under Mouse Kidney Capsule

To demonstrate that the human definitive endoderm cells produced using the methods described herein are capable of responding to differentiation factors so as to produce cells that are derived from the gut tube, such human definitive endoderm cells were subjected to an in vivo differentiation protocol.

Human definitive endoderm cells were produced as described in the foregoing Examples. Such cells were harvested and transplanted under the kidney capsule of immunocompromised mice using standard procedures. After three weeks, the mice were sacrificed and the transplanted tissue was removed, sectioned and subjected to histological and immunocytochemical analysis.

FIGS. 35A-D show that after three weeks post-transplantation, the human definitive endoderm cells differentiated into cells and cellular structures derived from the gut tube. In particular, FIG. 35A shows hematoxylin and eosin stained sections of transplanted human definitive endoderm tissue that has differentiated into gut-tube-like structures. FIG. 35B shows a transplanted human definitive endoderm section immunostained with antibody to hepatocyte specific antigen (HSA). This result indicates that the human definitive endoderm cells are capable of differentiating into liver or liver precursor cells. FIGS. 35C and 35D show a transplanted human definitive endoderm section immunostained with antibody to villin and antibody to caudal type homeobox transcription factor 2 (CDX2), respectively. These results indicate that the human definitive endoderm cells are capable of differentiating into intestinal cells or intestinal cell precursors.

Example 16 Identification of Differentiation Factors Capable of Promoting the Differentiation of Human Definitive Endoderm Cells In Vitro

To exemplify the differentiation factor screening methods described herein, populations of human definitive endoderm cells produced using the methods described herein were separately provided with several candidate differentiation factors while determining the normalized expression levels of certain marker gene products at various time points.

Human definitive endoderm cells were produced as described in the foregoing Examples. In brief, hESCs cells were grown in the presence of 100 ng/ml activin A in low serum RPMI medium for four days, wherein the fetal bovine serum (FBS) concentration on day 1 was 0%, on day 2 was 0.2% and on days 3-4 was 2%. After formation of definitive endoderm, beginning on day 5 and ending on day 10, cell populations maintained in individual plates in RPMI containing 0.2% FBS were treated with one of: Wnt3A at 20 ng/ml, FGF2 at 5 ng/ml or FGF2 at 100 ng/ml. The expression of marker gene products for albumin, PROX1 and TITF1 were quantitated using Q-PCR.

FIG. 36A shows that expression of the albumin gene product (a marker for liver precursors and liver cells) substantially increased on days 9 and 10 in response to FGF2 at 5 ng/ml as compared to expression in definitive endoderm cells on day 4 prior to treatment with this differentiation factor. Expression of the albumin gene product was also increased in response to 20 ng/ml Wnt3A on days 9 and 10 as compared to expression in untreated definitive endoderm cells, however, the increase was not as large as that observed for the 5 ng/ml FGF2 treatment. Of particular significance is the observation that the expression of the albumin gene product was not increased on days 9 and 10 in response to FGF2 at 100 ng/ml as compared to expression in definitive endoderm cells on day 4. Similar results were seen with the PROX1 marker (a second marker for liver precursors and liver cells) as shown in FIG. 36B. FIG. 36C shows that in cell populations provided with 100 ng/ml FGF2, expression of the TITF1 marker gene substantially increased on days 7, 9 and 10 as compared to expression in definitive endoderm cells on day 4 prior to treatment with this differentiation factor, but FGF2 at 5 ng/ml had very little effect on expression of this gene product as compared to untreated definitive endoderm. TITF1 is a marker expressed in developing lung and thyroid cells. Taken together, the results shown in FIGS. 36A-C indicate that the concentration at which the candidate differentiation factor is provided to the cell population can affect the differentiation fate of definitive endoderm cells in vitro.

The methods, compositions, and devices described herein are presently representative of preferred embodiments and are exemplary and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art which are encompassed within the spirit of the invention and are defined by the scope of the disclosure. Accordingly, it will be apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention.

As used in the claims below and throughout this disclosure, by the phrase “consisting essentially of” is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.

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What is claimed is:
 1. An isolated human cell population wherein at least 20% of cells in said cell population form an ex vivo reagent-cell complex comprising: a human definitive endoderm cell expressing a marker selected from the group consisting of CALCR, CMKOR1, CXCR4, GPR37, NTN4, RTN4RL1, SLC5A9, SLC40A1, and TRPA1, said definitive endoderm cell being a multipotent cell that can differentiate into cells of the gut tube or organs derived therefrom; and a reagent bound to said marker.
 2. The reagent cell complex of claim 1, wherein said marker comprises a polypeptide selected from the group consisting of CXCR4, GPR37, NTN4, RTN4RL1, SLC40A1, SLC5A9 and TRPA1.
 3. The human cell population of claim 1, wherein at least 40% of said human cells form said ex vivo reagent-cell complex.
 4. The human cell population of claim 1, wherein at least 60% of said human cells form said ex vivo reagent-cell complex.
 5. The human cell population of claim 1, wherein at least 80% of said human cells form said ex vivo reagent-cell complex.
 6. An isolated human cell population wherein at least 20% of cells in said cell population form an ex vivo reagent-cell complex comprising: a human definitive endoderm cell expressing CXCR4, said definitive endoderm cell being a multipotent cell that can differentiate into cells of the gut tube or organs derived therefrom and a reagent bound to CXCR4.
 7. The human cell population of claim 6, wherein at least 40% of said human cells form said ex vivo reagent-cell complex complexes.
 8. The human cell population of claim 6, wherein at least 60% of said human cells form said ex vivo reagent-cell complex.
 9. The human cell population of claim 6, wherein at least 80% of said human cells form said ex vivo reagent-cell complex. 